U1 small nuclear ribonucleoprotein C

Overview
NameU1 small nuclear ribonucleoprotein C
Smed IDSMED30023086
Length (bp)760
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of U1 small nuclear ribonucleoprotein C (SMED30023086) t-SNE clustered cells

Violin plots show distribution of expression levels for U1 small nuclear ribonucleoprotein C (SMED30023086) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of U1 small nuclear ribonucleoprotein C (SMED30023086) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for U1 small nuclear ribonucleoprotein C (SMED30023086) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020




SMED30023086

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30023086h1SMcG0003680 dd_Smed_v4_3772_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023086h1SMcG0003680 dd_Smed_v4_3772_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30023086h1SMcG0003680 dd_Smed_v4_3772_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023086h1SMcG0003680 dd_Smed_v4_3772_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30023086h1SMcG0003680 dd_Smed_v4_3772_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30023086h1SMcG0003680 dd_Smed_v4_3772_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023086h1SMcG0003680 dd_Smed_v4_3772_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Human
Match: SNRPC (small nuclear ribonucleoprotein polypeptide C [Source:HGNC Symbol;Acc:HGNC:11157])

HSP 1 Score: 106.686 bits (265), Expect = 6.399e-28
Identity = 42/61 (68.85%), Postives = 55/61 (90.16%), Query Frame = 3
Query:   75 FRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            FR+YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:   23 FRFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 83          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Human
Match: SNRPC (small nuclear ribonucleoprotein polypeptide C [Source:HGNC Symbol;Acc:HGNC:11157])

HSP 1 Score: 102.834 bits (255), Expect = 8.735e-27
Identity = 40/60 (66.67%), Postives = 54/60 (90.00%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            ++YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:    3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 62          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Celegans
Match: F08B4.7 (U1 small nuclear ribonucleoprotein C [Source:UniProtKB/Swiss-Prot;Acc:P90815])

HSP 1 Score: 108.227 bits (269), Expect = 2.129e-29
Identity = 47/73 (64.38%), Postives = 56/73 (76.71%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPP 296
            +YYCDYCDTFLTHDSPSVRKTH GGR H+DNVR +YQ+W+E Q QKLVDQT  +F   R+ G   R  +G+ P
Sbjct:    3 KYYCDYCDTFLTHDSPSVRKTHNGGRKHKDNVRMFYQKWMEDQAQKLVDQTARAFATNRMQGAVPRTTMGMAP 75          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Fly
Match: snRNP-U1-C (gene:FBgn0261792 transcript:FBtr0083720)

HSP 1 Score: 105.145 bits (261), Expect = 3.813e-28
Identity = 43/60 (71.67%), Postives = 52/60 (86.67%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            +YYCDYCDT+LTHDSPSVRKTHC GR HRDNV+ YYQ+W+E+Q Q L+D TT +FK G+I
Sbjct:    3 KYYCDYCDTYLTHDSPSVRKTHCTGRKHRDNVKFYYQKWMEEQAQHLIDATTAAFKAGKI 62          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Zebrafish
Match: snrpc (small nuclear ribonucleoprotein polypeptide C [Source:NCBI gene;Acc:192330])

HSP 1 Score: 103.605 bits (257), Expect = 3.095e-27
Identity = 40/60 (66.67%), Postives = 54/60 (90.00%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            ++YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:    3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 62          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Xenopus
Match: snrpc (small nuclear ribonucleoprotein polypeptide C [Source:NCBI gene;Acc:549352])

HSP 1 Score: 104.375 bits (259), Expect = 5.222e-27
Identity = 42/68 (61.76%), Postives = 57/68 (83.82%), Query Frame = 3
Query:   54 VYIINVQFRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            V  I +  ++YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:   35 VRAIRIMPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 102          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Mouse
Match: Snrpc (U1 small nuclear ribonucleoprotein C [Source:MGI Symbol;Acc:MGI:109489])

HSP 1 Score: 102.449 bits (254), Expect = 9.782e-27
Identity = 40/60 (66.67%), Postives = 54/60 (90.00%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            ++YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:    3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 62          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Mouse
Match: Snrpc (U1 small nuclear ribonucleoprotein C [Source:MGI Symbol;Acc:MGI:109489])

HSP 1 Score: 102.449 bits (254), Expect = 9.782e-27
Identity = 40/60 (66.67%), Postives = 54/60 (90.00%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            ++YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:    3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 62          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Mouse
Match: Snrpc (U1 small nuclear ribonucleoprotein C [Source:MGI Symbol;Acc:MGI:109489])

HSP 1 Score: 102.449 bits (254), Expect = 1.537e-26
Identity = 40/59 (67.80%), Postives = 53/59 (89.83%), Query Frame = 3
Query:   81 YYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            +YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:   27 FYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 85          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Mouse
Match: Snrpc (U1 small nuclear ribonucleoprotein C [Source:MGI Symbol;Acc:MGI:109489])

HSP 1 Score: 72.0182 bits (175), Expect = 2.734e-15
Identity = 28/45 (62.22%), Postives = 39/45 (86.67%), Query Frame = 3
Query:  123 PSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            PSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:   16 PSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 60          
BLAST of U1 small nuclear ribonucleoprotein C vs. UniProt/SwissProt
Match: sp|Q298E0|RU1C_DROPS (U1 small nuclear ribonucleoprotein C OS=Drosophila pseudoobscura pseudoobscura OX=46245 GN=snRNP-U1-C PE=3 SV=1)

HSP 1 Score: 111.309 bits (277), Expect = 2.091e-29
Identity = 52/86 (60.47%), Postives = 63/86 (73.26%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI-----PGGPIRAP-----LGLPPPGM 305
            +YYCDYCDT+LTHDSPSVRKTHC GR HRDNV+ YYQ+W+E+Q Q L+D TT +FK G+I      GGP  AP     + +PPP M
Sbjct:    3 KYYCDYCDTYLTHDSPSVRKTHCTGRKHRDNVKFYYQKWMEEQAQHLIDATTAAFKAGKITNNPFAGGPSSAPPKPSGVSIPPPNM 88          
BLAST of U1 small nuclear ribonucleoprotein C vs. UniProt/SwissProt
Match: sp|Q16IW3|RU1C_AEDAE (U1 small nuclear ribonucleoprotein C OS=Aedes aegypti OX=7159 GN=AAEL013527 PE=3 SV=1)

HSP 1 Score: 109.768 bits (273), Expect = 8.758e-29
Identity = 48/81 (59.26%), Postives = 61/81 (75.31%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIP-----GGPIRAPLGLPPPGM 305
            +YYCDYCDT+LTHDSPSVRKTHC GR H+DNV+ YYQ+W+E+Q Q L+D TT +FK G+I       GP +  + +PPP M
Sbjct:    3 KYYCDYCDTYLTHDSPSVRKTHCTGRKHKDNVKFYYQKWMEEQAQHLIDATTAAFKAGKIAQNPFSAGPPKPNVAIPPPSM 83          
BLAST of U1 small nuclear ribonucleoprotein C vs. UniProt/SwissProt
Match: sp|F7ARS3|RU1C_MONDO (U1 small nuclear ribonucleoprotein C OS=Monodelphis domestica OX=13616 GN=SNRPC PE=3 SV=1)

HSP 1 Score: 108.997 bits (271), Expect = 1.329e-28
Identity = 48/73 (65.75%), Postives = 60/73 (82.19%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRA-PLGLP 293
            ++YCDYCDT+LTHDSPSVRKTHC GR H++NVR YYQ+W+E+Q Q L+D+TT +F+QGRIP     A PLG P
Sbjct:    3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVRDYYQKWMEEQAQSLIDKTTTAFQQGRIPPNLFSAPPLGGP 75          
BLAST of U1 small nuclear ribonucleoprotein C vs. UniProt/SwissProt
Match: sp|C3Z1P5|RU1C_BRAFL (U1 small nuclear ribonucleoprotein C OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_69314 PE=3 SV=1)

HSP 1 Score: 110.923 bits (276), Expect = 1.559e-28
Identity = 43/64 (67.19%), Postives = 56/64 (87.50%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGP 269
            +Y+CDYCDT+LTHDSPSVRKTHC GR H++NVR YYQ+W+E+Q Q+L+DQTT +F+ G+IP  P
Sbjct:    3 KYFCDYCDTYLTHDSPSVRKTHCNGRKHKENVRVYYQKWMEEQAQQLIDQTTAAFQAGKIPNNP 66          
BLAST of U1 small nuclear ribonucleoprotein C vs. UniProt/SwissProt
Match: sp|Q7PXU6|RU1C_ANOGA (U1 small nuclear ribonucleoprotein C OS=Anopheles gambiae OX=7165 GN=AGAP001584 PE=3 SV=2)

HSP 1 Score: 108.997 bits (271), Expect = 1.642e-28
Identity = 47/81 (58.02%), Postives = 61/81 (75.31%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIP-----GGPIRAPLGLPPPGM 305
            +YYCDYCDT+LTHDSPSVRKTHC GR H+DNV+ YYQ+W+E+Q Q L+D TT ++K G+I       GP +  + +PPP M
Sbjct:    3 KYYCDYCDTYLTHDSPSVRKTHCTGRKHKDNVKFYYQKWMEEQAQHLIDATTAAYKAGKIAPNPFTAGPPKPNISIPPPTM 83          
BLAST of U1 small nuclear ribonucleoprotein C vs. TrEMBL
Match: A0A4E0RM70 (U1 small nuclear ribonucleoprotein C OS=Fasciola hepatica OX=6192 GN=D915_007318 PE=3 SV=1)

HSP 1 Score: 131.724 bits (330), Expect = 4.919e-35
Identity = 55/77 (71.43%), Postives = 69/77 (89.61%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPPPGMF 308
            +YYCDYCDTFLTHDSPSVRKTHCGGR H+DNV++YYQ+WLE+QVQKLVD T+E++KQG++P     AP+G+PPPG+ 
Sbjct:    3 KYYCDYCDTFLTHDSPSVRKTHCGGRNHKDNVKEYYQKWLEEQVQKLVDHTSEAYKQGKVPPPLFGAPMGMPPPGLM 79          
BLAST of U1 small nuclear ribonucleoprotein C vs. TrEMBL
Match: A0A074ZY03 (U1 small nuclear ribonucleoprotein C OS=Opisthorchis viverrini OX=6198 GN=T265_01556 PE=3 SV=1)

HSP 1 Score: 129.413 bits (324), Expect = 4.791e-34
Identity = 55/76 (72.37%), Postives = 68/76 (89.47%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPPPGM 305
            +YYCDYCDT+LTHDSPSVRKTHCGGR H+DNVR YYQ+WLE+QVQKLVD T+E++KQG++P     +PLG+PPPG+
Sbjct:    3 KYYCDYCDTYLTHDSPSVRKTHCGGRNHKDNVRDYYQKWLEEQVQKLVDHTSEAYKQGKMPPPLFGSPLGMPPPGL 78          
BLAST of U1 small nuclear ribonucleoprotein C vs. TrEMBL
Match: A0A4S2LY09 (U1 small nuclear ribonucleoprotein C OS=Opisthorchis felineus OX=147828 GN=CRM22_004241 PE=3 SV=1)

HSP 1 Score: 129.028 bits (323), Expect = 6.008e-34
Identity = 55/76 (72.37%), Postives = 68/76 (89.47%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPPPGM 305
            +YYCDYCDT+LTHDSPSVRKTHCGGR H+DNVR YYQ+WLE+QVQKLVD T+E++KQG++P     +PLG+PPPG+
Sbjct:    3 KYYCDYCDTYLTHDSPSVRKTHCGGRNHKDNVRDYYQKWLEEQVQKLVDHTSEAYKQGKMPPPLFGSPLGMPPPGL 78          
BLAST of U1 small nuclear ribonucleoprotein C vs. TrEMBL
Match: A0A419PKY8 (U1 small nuclear ribonucleoprotein C OS=Clonorchis sinensis OX=79923 GN=CSKR_722s PE=3 SV=1)

HSP 1 Score: 134.035 bits (336), Expect = 6.371e-34
Identity = 57/81 (70.37%), Postives = 72/81 (88.89%), Query Frame = 3
Query:   63 INVQFRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPPPGM 305
            I+++ RYYCDYCDT+LTHDSPSVRKTHCGGR H+DNVR YYQ+WLE+QVQKLVD T+E++KQG++P     +PLG+PPPG+
Sbjct:  171 IHLRLRYYCDYCDTYLTHDSPSVRKTHCGGRNHKDNVRDYYQKWLEEQVQKLVDHTSEAYKQGKMPPPLFGSPLGMPPPGL 251          
BLAST of U1 small nuclear ribonucleoprotein C vs. TrEMBL
Match: G7Y9F2 (U1 small nuclear ribonucleoprotein C OS=Clonorchis sinensis OX=79923 GN=CLF_103260 PE=3 SV=1)

HSP 1 Score: 135.191 bits (339), Expect = 2.003e-32
Identity = 57/81 (70.37%), Postives = 72/81 (88.89%), Query Frame = 3
Query:   63 INVQFRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPPPGM 305
            I+++ RYYCDYCDT+LTHDSPSVRKTHCGGR H+DNVR YYQ+WLE+QVQKLVD T+E++KQG++P     +PLG+PPPG+
Sbjct:  367 IHLRLRYYCDYCDTYLTHDSPSVRKTHCGGRNHKDNVRDYYQKWLEEQVQKLVDHTSEAYKQGKMPPPLFGSPLGMPPPGL 447          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Cavefish
Match: snrpc (small nuclear ribonucleoprotein polypeptide C [Source:NCBI gene;Acc:111193750])

HSP 1 Score: 103.605 bits (257), Expect = 4.848e-27
Identity = 43/75 (57.33%), Postives = 58/75 (77.33%), Query Frame = 3
Query:   33 ENRKYSTVYIINVQFRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            E R    V +     ++YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:   11 EQRGGLCVCVCVKMPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 85          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Cavefish
Match: snrpc (small nuclear ribonucleoprotein polypeptide C [Source:NCBI gene;Acc:111193750])

HSP 1 Score: 94.7449 bits (234), Expect = 4.921e-24
Identity = 36/55 (65.45%), Postives = 49/55 (89.09%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESF 242
            ++YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+T++S 
Sbjct:    3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTSKSL 57          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Sea Lamprey
Match: snrpc (small nuclear ribonucleoprotein polypeptide C [Source:NCBI gene;Acc:192330])

HSP 1 Score: 112.849 bits (281), Expect = 1.149e-31
Identity = 45/67 (67.16%), Postives = 58/67 (86.57%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRA 278
            +YYCDYCDT+LTHDSPSVRKTHCGGR H++NV+ YYQ+W+E+Q Q L+DQTT +F+QG++  GP  A
Sbjct:    3 KYYCDYCDTYLTHDSPSVRKTHCGGRKHKENVKDYYQKWMEEQAQNLIDQTTAAFQQGKMGSGPSAA 69          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Yeast
Match: YHC1 (Component of the U1 snRNP complex required for pre-mRNA splicing; putative ortholog of human U1C protein, which is involved in formation of a complex between U1 snRNP and the pre-mRNA 5' splice site [Source:SGD;Acc:S000004289])

HSP 1 Score: 47.3654 bits (111), Expect = 4.750e-7
Identity = 23/59 (38.98%), Postives = 33/59 (55.93%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGR 254
            RYYC+YC ++LTHD+ SVRK+H  G+ H      YY+      + K   +     K+GR
Sbjct:    3 RYYCEYCHSYLTHDTLSVRKSHLVGKNHLRITADYYRNKARDIINKHNHKRRHIGKRGR 61          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Nematostella
Match: EDO37851 (U1 small nuclear ribonucleoprotein C [Source:UniProtKB/Swiss-Prot;Acc:A7SEP9])

HSP 1 Score: 95.9005 bits (237), Expect = 4.943e-25
Identity = 40/56 (71.43%), Postives = 49/56 (87.50%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFK 245
            +YYCDYCDTFLTHDSPSVRKTH  GR H++NVR YYQ+W+E+Q Q L+DQTT +F+
Sbjct:    3 KYYCDYCDTFLTHDSPSVRKTHNNGRKHKENVRFYYQKWMEEQAQTLIDQTTAAFQ 58          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Medaka
Match: snrpc (small nuclear ribonucleoprotein polypeptide C [Source:NCBI gene;Acc:101158847])

HSP 1 Score: 108.227 bits (269), Expect = 3.017e-28
Identity = 41/66 (62.12%), Postives = 56/66 (84.85%), Query Frame = 3
Query:   60 IINVQFRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            + +V   +YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:   79 MFDVTTSFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 144          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Medaka
Match: snrpc (small nuclear ribonucleoprotein polypeptide C [Source:NCBI gene;Acc:101158847])

HSP 1 Score: 102.834 bits (255), Expect = 4.158e-27
Identity = 40/60 (66.67%), Postives = 54/60 (90.00%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRI 257
            ++YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+TT +F+QG+I
Sbjct:    3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKI 62          
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Medaka
Match: snrpc (small nuclear ribonucleoprotein polypeptide C [Source:NCBI gene;Acc:101158847])

HSP 1 Score: 96.6709 bits (239), Expect = 1.233e-24
Identity = 37/55 (67.27%), Postives = 50/55 (90.91%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESF 242
            R+YCDYCDT+LTHDSPSVRKTHC GR H++NV+ YYQ+W+E+Q Q L+D+T+++F
Sbjct:   18 RFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTSKTF 72          
BLAST of U1 small nuclear ribonucleoprotein C vs. Planmine SMEST
Match: SMESG000010972.1 (SMESG000010972.1)

HSP 1 Score: 273.863 bits (699), Expect = 3.641e-94
Identity = 150/150 (100.00%), Postives = 150/150 (100.00%), Query Frame = 3
Query:   21 MPKYENRKYSTVYIINVQFRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPPPGMFPRRXXXXXXXXXXXXXXXXVIQQTSNGIHTIPVSTANPVHGQFPPAWNPVPQTM 470
            MPKYENRKYSTVYIINVQFRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPPPGMFPRRPLLGMQGFQGGQLPPPVIQQTSNGIHTIPVSTANPVHGQFPPAWNPVPQTM
Sbjct:    1 MPKYENRKYSTVYIINVQFRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPPPGMFPRRPLLGMQGFQGGQLPPPVIQQTSNGIHTIPVSTANPVHGQFPPAWNPVPQTM 150          
BLAST of U1 small nuclear ribonucleoprotein C vs. Planmine SMEST
Match: SMESG000041687.1 (SMESG000041687.1)

HSP 1 Score: 84.7297 bits (208), Expect = 1.160e-20
Identity = 37/72 (51.39%), Postives = 49/72 (68.06%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLP 293
            +YYCDYCD FLTHDSPSVRKTH  G+FHRDN + YY   L++Q QK+V++   +F   ++   P+     LP
Sbjct:    3 KYYCDYCDMFLTHDSPSVRKTHLEGKFHRDNYQNYYLNVLKEQAQKMVNEELSNFNH-QLLMNPVTPMCSLP 73          
BLAST of U1 small nuclear ribonucleoprotein C vs. Planmine SMEST
Match: SMESG000005764.1 (SMESG000005764.1)

HSP 1 Score: 84.7297 bits (208), Expect = 1.890e-20
Identity = 35/72 (48.61%), Postives = 51/72 (70.83%), Query Frame = 3
Query:   78 RYYCDYCDTFLTHDSPSVRKTHCGGRFHRDNVRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLP 293
            +YYCDYCD FLTHDSPSVRKTH  G+FHR+N + YY + L++Q QK+V++   +F   ++   P+   + +P
Sbjct:    3 KYYCDYCDMFLTHDSPSVRKTHLEGKFHRENYQNYYLKVLKEQAQKMVNEELANFNH-QLLMNPVAPMMSVP 73          
The following BLAST results are available for this feature:
BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 2
Match NameE-valueIdentityDescription
SNRPC6.399e-2868.85small nuclear ribonucleoprotein polypeptide C [Sou... [more]
SNRPC8.735e-2766.67small nuclear ribonucleoprotein polypeptide C [Sou... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1
Match NameE-valueIdentityDescription
F08B4.72.129e-2964.38U1 small nuclear ribonucleoprotein C [Source:UniP... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
snRNP-U1-C3.813e-2871.67gene:FBgn0261792 transcript:FBtr0083720[more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
snrpc3.095e-2766.67small nuclear ribonucleoprotein polypeptide C [Sou... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
snrpc5.222e-2761.76small nuclear ribonucleoprotein polypeptide C [Sou... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 4
Match NameE-valueIdentityDescription
Snrpc9.782e-2766.67U1 small nuclear ribonucleoprotein C [Source:MGI S... [more]
Snrpc9.782e-2766.67U1 small nuclear ribonucleoprotein C [Source:MGI S... [more]
Snrpc1.537e-2667.80U1 small nuclear ribonucleoprotein C [Source:MGI S... [more]
Snrpc2.734e-1562.22U1 small nuclear ribonucleoprotein C [Source:MGI S... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 5
Match NameE-valueIdentityDescription
sp|Q298E0|RU1C_DROPS2.091e-2960.47U1 small nuclear ribonucleoprotein C OS=Drosophila... [more]
sp|Q16IW3|RU1C_AEDAE8.758e-2959.26U1 small nuclear ribonucleoprotein C OS=Aedes aegy... [more]
sp|F7ARS3|RU1C_MONDO1.329e-2865.75U1 small nuclear ribonucleoprotein C OS=Monodelphi... [more]
sp|C3Z1P5|RU1C_BRAFL1.559e-2867.19U1 small nuclear ribonucleoprotein C OS=Branchiost... [more]
sp|Q7PXU6|RU1C_ANOGA1.642e-2858.02U1 small nuclear ribonucleoprotein C OS=Anopheles ... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4E0RM704.919e-3571.43U1 small nuclear ribonucleoprotein C OS=Fasciola h... [more]
A0A074ZY034.791e-3472.37U1 small nuclear ribonucleoprotein C OS=Opisthorch... [more]
A0A4S2LY096.008e-3472.37U1 small nuclear ribonucleoprotein C OS=Opisthorch... [more]
A0A419PKY86.371e-3470.37U1 small nuclear ribonucleoprotein C OS=Clonorchis... [more]
G7Y9F22.003e-3270.37U1 small nuclear ribonucleoprotein C OS=Clonorchis... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
snrpc4.848e-2757.33small nuclear ribonucleoprotein polypeptide C [Sou... [more]
snrpc4.921e-2465.45small nuclear ribonucleoprotein polypeptide C [Sou... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
snrpc1.149e-3167.16small nuclear ribonucleoprotein polypeptide C [Sou... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
YHC14.750e-738.98Component of the U1 snRNP complex required for pre... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO378514.943e-2571.43U1 small nuclear ribonucleoprotein C [Source:UniP... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 3
Match NameE-valueIdentityDescription
snrpc3.017e-2862.12small nuclear ribonucleoprotein polypeptide C [Sou... [more]
snrpc4.158e-2766.67small nuclear ribonucleoprotein polypeptide C [Sou... [more]
snrpc1.233e-2467.27small nuclear ribonucleoprotein polypeptide C [Sou... [more]
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BLAST of U1 small nuclear ribonucleoprotein C vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000010972.13.641e-94100.00SMESG000010972.1[more]
SMESG000041687.11.160e-2051.39SMESG000041687.1[more]
SMESG000005764.11.890e-2048.61SMESG000005764.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023086 ID=SMED30023086|Name=U1 small nuclear ribonucleoprotein C|organism=Schmidtea mediterranea sexual|type=transcript|length=760bp
CTATATAAATCTTATATGTTATGCCCAAGTATGAAAATCGTAAATATTCA
ACCGTTTACATAATAAATGTTCAATTCAGGTACTATTGTGATTATTGCGA
TACATTTCTCACACATGACTCACCTTCGGTTCGAAAAACACATTGTGGAG
GGAGATTTCATCGTGATAATGTAAGAAAATATTATCAAGAGTGGTTGGAA
CAACAAGTACAGAAATTGGTCGACCAAACAACGGAGTCATTCAAACAAGG
CCGGATCCCAGGGGGTCCAATTAGAGCTCCTTTAGGGTTACCACCACCAG
GAATGTTTCCACGCAGACCTCTTCTCGGTATGCAGGGTTTTCAAGGAGGA
CAATTACCGCCACCAGTCATTCAACAAACTTCTAATGGCATTCATACAAT
TCCAGTTTCAACAGCAAATCCTGTTCATGGGCAGTTTCCTCCTGCTTGGA
ATCCAGTTCCTCAAACAATGCCACCATTTTTCCCTCAATTCAGTAAATAG
TCCAGTTTCCGTTTTAATCATTTTCAATATACTATTGTCGTTTCTTTTAA
TCCATGTTGTCGATATTCTCCCGTTGATAAATTTATTTACTTATCGTACT
TTGGCAATGGTTATATGTTACTTAAATATCAGAATATGACTCGATGTTAG
TTTTCAGTTAAAACTGAATTCTAATTTTATGTTTAGAAGGTAAACAATAT
TTGTTAATGATTATGTTTTAGATTTACTAAGGAATCTCTCTTTAAGACTT
TACTTGTCAG
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protein sequence of SMED30023086-orf-1

>SMED30023086-orf-1 ID=SMED30023086-orf-1|Name=SMED30023086-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=160bp
MPKYENRKYSTVYIINVQFRYYCDYCDTFLTHDSPSVRKTHCGGRFHRDN
VRKYYQEWLEQQVQKLVDQTTESFKQGRIPGGPIRAPLGLPPPGMFPRRP
LLGMQGFQGGQLPPPVIQQTSNGIHTIPVSTANPVHGQFPPAWNPVPQTM
PPFFPQFSK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR017340U1_snRNP-C
IPR036236Znf_C2H2_sf
IPR003604Matrin/U1-like-C_Znf_C2H2
IPR013085U1-CZ_Znf_C2H2
IPR000690Matrin/U1-C_Znf_C2H2
IPR020846MFS_dom
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0008270zinc ion binding
GO:0003723RNA binding
GO:0003729mRNA binding
GO:0030619U1 snRNA binding
GO:0046872metal ion binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0000243commitment complex
GO:0005685U1 snRNP
GO:0016020membrane
GO:0016021integral component of membrane
GO:0019013viral nucleocapsid
GO:0030529intracellular ribonucleoprotein complex
GO:0071004U2-type prespliceosome
Vocabulary: biological process
TermDefinition
GO:0000387spliceosomal snRNP assembly
GO:0000395mRNA 5'-splice site recognition
GO:0000398mRNA splicing, via spliceosome
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR003604Matrin/U1-C-like, C2H2-type zinc fingerSMARTSM00451ZnF_U1_5coord: 19..55
e-value: 1.9E-9
score: 47.4
IPR017340U1 small nuclear ribonucleoprotein CPIRSFPIRSF037969U1-Ccoord: 20..159
e-value: 4.7E-27
score: 93.9
IPR017340U1 small nuclear ribonucleoprotein CPANTHERPTHR31148FAMILY NOT NAMEDcoord: 21..152
NoneNo IPR availableGENE3DG3DSA:3.30.160.60coord: 20..79
e-value: 1.0E-29
score: 104.4
IPR013085U1-C, C2H2-type zinc fingerPFAMPF06220zf-U1coord: 21..56
e-value: 1.1E-18
score: 66.7
IPR000690Matrin/U1-C, C2H2-type zinc fingerPROSITEPS50171ZF_MATRINcoord: 22..54
score: 13.301
IPR036236Zinc finger C2H2 superfamilySUPERFAMILYSSF57667beta-beta-alpha zinc fingerscoord: 21..76