U4/U6 small nuclear ribonucleoprotein Prp4

Overview
NameU4/U6 small nuclear ribonucleoprotein Prp4
Smed IDSMED30011408
Length (bp)786
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 U4/U6 small nuclear ribonucleoprotein Prp4 (SMED30011408) t-SNE clustered cells

Violin plots show distribution of expression levels for U4/U6 small nuclear ribonucleoprotein Prp4 (SMED30011408) 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 U4/U6 small nuclear ribonucleoprotein Prp4 (SMED30011408) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for U4/U6 small nuclear ribonucleoprotein Prp4 (SMED30011408) 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.
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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



SMED30011408

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30011408h1SMcG0019030 dd_Smed_v4_5808_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011408h1SMcG0019030 dd_Smed_v4_5808_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30011408h1SMcG0019030 dd_Smed_v4_5808_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
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Human
Match: EXOSC5 (exosome component 5 [Source:HGNC Symbol;Acc:HGNC:24662])

HSP 1 Score: 51.2174 bits (121), Expect = 4.242e-7
Identity = 38/140 (27.14%), Postives = 70/140 (50.00%), Query Frame = 2 
Query:  110 GSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-----NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHEIGTVAWDTIGKN 514
            GS+S+   D  V+  +YGP  VK SKE   +A L+V +  + G      K+++ L    I+ T E ++  + +P+T I + +++VS   D+ + +    N+  +AL++A   M+        ++D    GT+  D   K 
Sbjct:   43 GSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERL----IRNTCEAVVLGTLHPRTSITVVLQVVS---DAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSD--GTLVLDPTSKQ 173
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Zebrafish
Match: exosc5 (exosome component 5 [Source:ZFIN;Acc:ZDB-GENE-060503-675])

HSP 1 Score: 47.7506 bits (112), Expect = 3.184e-6
Identity = 38/145 (26.21%), Postives = 76/145 (52.41%), Query Frame = 2 
Query:   74 PLLAEVG-----LYDCTGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAGNKN-KDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMK---CSLSASTVSVDGHEI 481
            P+L E G     L    GSS++   D  ++  +YGP  VK SKE   +A ++V I  + G  + ++   +  +++T E  L L+ +P++ + + +++V    D  + ++   N+  +AL++A   M    CS++ + +S +G  I
Sbjct:   12 PVLREYGSEQSLLSRPDGSSTFVQGDTSILAGVYGPAEVKVSKEIYDRATVEVLIQPKMGLPSVRERAREQCVRETCEAALLLTLHPRSSLTVILQVVH---DDGSLLSCCLNAACMALMDAGLPMSRLFCSVTCA-ISKEGQII 152
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Zebrafish
Match: exosc5 (exosome component 5 [Source:ZFIN;Acc:ZDB-GENE-060503-675])

HSP 1 Score: 47.7506 bits (112), Expect = 3.184e-6
Identity = 38/145 (26.21%), Postives = 76/145 (52.41%), Query Frame = 2 
Query:   74 PLLAEVG-----LYDCTGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAGNKN-KDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMK---CSLSASTVSVDGHEI 481
            P+L E G     L    GSS++   D  ++  +YGP  VK SKE   +A ++V I  + G  + ++   +  +++T E  L L+ +P++ + + +++V    D  + ++   N+  +AL++A   M    CS++ + +S +G  I
Sbjct:   12 PVLREYGSEQSLLSRPDGSSTFVQGDTSILAGVYGPAEVKVSKEIYDRATVEVLIQPKMGLPSVRERAREQCVRETCEAALLLTLHPRSSLTVILQVVH---DDGSLLSCCLNAACMALMDAGLPMSRLFCSVTCA-ISKEGQII 152
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Xenopus
Match: EXOSC5 (exosome component 5 [Source:NCBI gene;Acc:100170617])

HSP 1 Score: 54.299 bits (129), Expect = 3.095e-8
Identity = 38/135 (28.15%), Postives = 71/135 (52.59%), Query Frame = 2 
Query:  110 GSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-----NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHEIGTVAWD 499
            GS+++   D  V+  +YGP  +K S+E   +A L+V +  + G      KN++ L    I++T E ++  S +P+T I I ++IVS   D+ + ++   N+  + L++A   M+      T ++D    GT+  D
Sbjct:   23 GSATFLQGDTSVMAGVYGPAEIKVSREIHNKATLEVILRPKTGLPAIQEKNQEQL----IRETCESVIIGSLHPRTSITIVLQIVS---DAGSLLSCCLNAACMGLMDAGLPMRALFCGVTCAMDND--GTITLD 148
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Mouse
Match: Exosc5 (exosome component 5 [Source:MGI Symbol;Acc:MGI:107889])

HSP 1 Score: 50.447 bits (119), Expect = 5.789e-7
Identity = 34/125 (27.20%), Postives = 66/125 (52.80%), Query Frame = 2 
Query:  110 GSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-----NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVD 469
            GS+S+   D  V+  +YGP  VK SKE   +A L+V +  + G      K+++ L    ++ T E ++  + +P+T I + +++VS   D+ + +    N+  +AL++A   M+      T ++D
Sbjct:   43 GSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERL----VRNTCEAVVLGALHPRTSITVVLQVVS---DAGSLLACCLNAACMALVDAGVPMRALFCGVTCALD 160
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Mouse
Match: Exosc5 (exosome component 5 [Source:MGI Symbol;Acc:MGI:107889])

HSP 1 Score: 50.447 bits (119), Expect = 5.789e-7
Identity = 34/125 (27.20%), Postives = 66/125 (52.80%), Query Frame = 2 
Query:  110 GSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-----NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVD 469
            GS+S+   D  V+  +YGP  VK SKE   +A L+V +  + G      K+++ L    ++ T E ++  + +P+T I + +++VS   D+ + +    N+  +AL++A   M+      T ++D
Sbjct:   43 GSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERL----VRNTCEAVVLGALHPRTSITVVLQVVS---DAGSLLACCLNAACMALVDAGVPMRALFCGVTCALD 160
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. UniProt/SwissProt
Match: sp|O42894|RRP46_SCHPO (Exosome complex component rrp46 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=rrp46 PE=3 SV=1)

HSP 1 Score: 55.0694 bits (131), Expect = 7.892e-8
Identity = 33/110 (30.00%), Postives = 59/110 (53.64%), Query Frame = 2 
Query:  110 GSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMK 436
            GSS W+     VI  + GP  VK   E + +A ++V +   +G  +  + ++ S I    E  + L+ YP+T+I++ ++I+  + D   T+ A+ N   LALL+A   +K
Sbjct:   12 GSSEWKQGSARVICGVNGPIDVKIRDERLNKATVEVLVQPVSGVAETLEKMISSRIVGILEDAIFLNTYPRTLIQVSIQII--EEDGTDTLAAVINGAVLALLDAGISLK 119
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. UniProt/SwissProt
Match: sp|Q9NQT4|EXOS5_HUMAN (Exosome complex component RRP46 OS=Homo sapiens OX=9606 GN=EXOSC5 PE=1 SV=1)

HSP 1 Score: 51.2174 bits (121), Expect = 2.037e-6
Identity = 38/140 (27.14%), Postives = 70/140 (50.00%), Query Frame = 2 
Query:  110 GSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-----NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHEIGTVAWDTIGKN 514
            GS+S+   D  V+  +YGP  VK SKE   +A L+V +  + G      K+++ L    I+ T E ++  + +P+T I + +++VS   D+ + +    N+  +AL++A   M+        ++D    GT+  D   K 
Sbjct:   43 GSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERL----IRNTCEAVVLGTLHPRTSITVVLQVVS---DAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSD--GTLVLDPTSKQ 173
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. UniProt/SwissProt
Match: sp|Q9CRA8|EXOS5_MOUSE (Exosome complex component RRP46 OS=Mus musculus OX=10090 GN=Exosc5 PE=1 SV=1)

HSP 1 Score: 50.447 bits (119), Expect = 4.050e-6
Identity = 34/125 (27.20%), Postives = 66/125 (52.80%), Query Frame = 2 
Query:  110 GSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-----NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVD 469
            GS+S+   D  V+  +YGP  VK SKE   +A L+V +  + G      K+++ L    ++ T E ++  + +P+T I + +++VS   D+ + +    N+  +AL++A   M+      T ++D
Sbjct:   43 GSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERL----VRNTCEAVVLGALHPRTSITVVLQVVS---DAGSLLACCLNAACMALVDAGVPMRALFCGVTCALD 160
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. TrEMBL
Match: A0A0R3U5E5 (RNase_PH domain-containing protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS1942 PE=4 SV=2)

HSP 1 Score: 77.7962 bits (190), Expect = 2.430e-13
Identity = 45/139 (32.37%), Postives = 76/139 (54.68%), Query Frame = 2 
Query:  101 DC--TGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSA---STVSVDGHEIGTVAWD 499
            DC  TGSS+W   + HV+  IYGP+    + E   +A LDV +   +G +   ++ ++ Y+ +  E+++ +  YP+    I++++VSG    P T+ A  N+++LALL     +K S+ A   S V  D   I T+A D
Sbjct:   13 DCNATGSSTWAFGNTHVLASIYGPKEASMANELTHRAFLDVSVLPVSGVHTMLESDMEFYLLQYLERLIDVKDYPRCQFNIRIQLVSGPPGHPMTMAACINALALALLQTSIPLKASVVAVCTSEVDADSRPI-TLAID 150
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. TrEMBL
Match: A0A0R3WNI6 (RNase_PH domain-containing protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS2311 PE=4 SV=1)

HSP 1 Score: 76.2554 bits (186), Expect = 8.139e-13
Identity = 42/130 (32.31%), Postives = 73/130 (56.15%), Query Frame = 2 
Query:  101 DC--TGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHEI 481
            DC  TGS+SW   D HV+  +YGP+    + E   +A +DV +   +G +   ++ ++ Y++   E+++ +  YP+    ++++I+SG +  PTT+ A  N++SLALL         L AS V+V   EI
Sbjct:   13 DCNATGSASWAFGDAHVMASVYGPKEASMANELTHRAYIDVSVLPVSGLHTPFESEMEFYLQNFLERLIDVKVYPRNQFGVRIQIISGLSGHPTTMAACVNALSLALLPTSI----PLHASVVAVCSSEI 138
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. TrEMBL
Match: A0A0R3SBX4 (RNase_PH domain-containing protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS2024 PE=4 SV=1)

HSP 1 Score: 76.2554 bits (186), Expect = 8.460e-13
Identity = 49/147 (33.33%), Postives = 79/147 (53.74%), Query Frame = 2 
Query:   50 IEDSNHVIPLLAEVGLYDC--TGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAGNKNK-DALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHEI 481
            +E SN    LL E+   DC  +GS +W   D HVI  +YGP+    + E   +A +DV I   +G     ++ ++ YI +  E+++ + KYP+    ++++IVSG +    T+ A  N+VSLALL         L+AS V+V   E+
Sbjct:    1 MERSN----LLVELN-TDCNASGSCTWAFGDAHVIASVYGPKEANMANELTHRACIDVSISPVSGFHTPCESEMELYITQLLERLIEVKKYPRNQFNVRIQIVSGISGHAVTMAACINAVSLALLQTAI----PLTASIVAVCSSEV 138
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. TrEMBL
Match: A0A5J4NLI1 (Uncharacterized protein OS=Paragonimus westermani OX=34504 GN=DEA37_0008051 PE=4 SV=1)

HSP 1 Score: 77.7962 bits (190), Expect = 1.301e-12
Identity = 42/134 (31.34%), Postives = 76/134 (56.72%), Query Frame = 2 
Query:   77 LLAEVGLYDCT--GSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAGNKN-KDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVD 469
            L  E+G  DC   GS++WE+E  HV   +YGP+  K   E   +A ++V + S  G    K+  L+ Y+    E+++ +  +P+T I  ++ IV+G+   P T+ A  N++SLALL +   ++ +++A   S++
Sbjct:    3 LFVELGT-DCNACGSATWELEGHHVTFSVYGPDEAKTQDELTHRACVEVIVTSAVGQHTLKETELECYLITFMERLIDVKSFPRTKISGRLCIVTGEASHPKTVAAALNAISLALLQSGLPLRATVAAVCTSIE 135
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. TrEMBL
Match: A0A0R3WBN1 (RNase_PH domain-containing protein OS=Taenia asiatica OX=60517 GN=TASK_LOCUS8058 PE=4 SV=1)

HSP 1 Score: 75.0998 bits (183), Expect = 1.936e-12
Identity = 38/120 (31.67%), Postives = 69/120 (57.50%), Query Frame = 2 
Query:  101 DC--TGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAG-NKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSA 451
            DC  TGSSSW     HV+  IYGP+    + E   +A +DV +   +G +   ++ ++ Y++   E+++ +  YP+    I+++I+SG +  P T+ A  N++SLALL+    ++ S+ A
Sbjct:   13 DCNATGSSSWAFGGAHVMASIYGPKEASMANELTHRAYIDVSVQPVSGLHTPFESDVEFYLQNFLERLIDVKVYPRNQFAIRIQIISGVSGHPATMAACINALSLALLSTSIPLQASVVA 132
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Yeast
Match: SKI6 (Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; has similarity to E. coli RNase PH and to human hRrp41p (EXOSC4) [Source:SGD;Acc:S000003427])

HSP 1 Score: 46.9802 bits (110), Expect = 7.239e-7
Identity = 39/162 (24.07%), Postives = 84/162 (51.85%), Query Frame = 2 
Query:   98 YDCTGSSSWEIEDDHVITRIYGPEGVK-QSKENVQQAILDVEIH---------SEAGNKNKDALL--QSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTV------------SVDGHEIGTVAWDTIGK 511
            +   GSS  E  ++ +IT + GP+  + +S+ +  +A+L+V ++         S++ +KN+  +L  Q+ + + FEK + L+ YP+T+I I++ ++         + ++ N ++LAL++A   M   +S  +V            S++ + + TV    +GK
Sbjct:   34 HAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLE---QDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGK 192
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Nematostella
Match: EDO43013 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RZV7])

HSP 1 Score: 58.5362 bits (140), Expect = 2.400e-10
Identity = 42/166 (25.30%), Postives = 80/166 (48.19%), Query Frame = 2 
Query:   77 LLAEVGLYD-CTGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAGNKN-KDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHE----------------IGTVAWDTIGKNLL 520
            +  E GL D   GSS +   D  V+   YGP  VK +KE + +A L+V    + G     + L++  I+ + E I+  + +P+  + I V++V    +S + ++   N+  LA+++A F M+C +   T ++   +                + T  +D++ +NLL
Sbjct:   18 MFCEHGLLDKADGSSKFAQGDTQVMAAAYGPVEVKLNKELIDRATLEVIFRPKIGIPGCSEKLVEGIIRNSCEPIVLTALHPRASLTIVVQVVQ---NSGSLLSCAVNAACLAMMDAGFPMRCMMCGITCAITEQDELVLDPTLEQERKATAVLTFVFDSVNQNLL 180
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Nematostella
Match: EDO42491 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S1D9])

HSP 1 Score: 46.2098 bits (108), Expect = 4.003e-6
Identity = 38/141 (26.95%), Postives = 71/141 (50.35%), Query Frame = 2 
Query:   77 LLAEVG-LYDCTGSSSWEIEDDHVITRIYGPEGVKQSKENVQ-QAILDV----------EIHSEAGNKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVS 463
            ++ +VG L    GS+  E+ +   +  +YGP  V+   + +  + +L+V          E   +     K   L   +++TFE  + ++ YP++ I I V+++  + D    +  I N+V+LAL+NA   +K  +SA TVS
Sbjct:   25 MVCKVGVLSQADGSAYIEMGNTKALATVYGPHEVQNKAKALHDRVLLNVQFGMATFSTGERKKKPRGDRKATELSMMVRRTFEAAILINLYPRSQIDIYVQVL--QADGGNHVACI-NAVTLALINAGIPLKDYVSACTVS 162
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Medaka
Match: exosc5 (exosome component 5 [Source:NCBI gene;Acc:101161262])

HSP 1 Score: 51.9878 bits (123), Expect = 9.384e-8
Identity = 30/123 (24.39%), Postives = 66/123 (53.66%), Query Frame = 2 
Query:  110 GSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAGNKN-KDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGH 475
            GS+S+   D  V+  +YGP  VK SKE   +A L+V +  + G  + ++   +  +++T E+ L L+ +P++ + + ++++    D  + ++   N+  +AL++A   M C     T ++  +
Sbjct:   26 GSASFVQGDTSVMAGVYGPAEVKVSKEIYDRATLEVLVQPKVGLPSVRERSQEQCVRETCEEALLLTLHPRSSLTLVLQVLH---DDGSLLSCCLNAACMALMDAGLPMSCLFCGVTCAISAY 145
[Close]
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Planmine SMEST
Match: SMESG000026944.1 (SMESG000026944.1)

HSP 1 Score: 414.846 bits (1065), Expect = 3.901e-149
Identity = 201/201 (100.00%), Postives = 201/201 (100.00%), Query Frame = 2 
Query:   41 MNSIEDSNHVIPLLAEVGLYDCTGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAGNKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHEIGTVAWDTIGKNLLFCYQSTNEYMNGEQIVPAIEDTFVDCCEISKMISAVLCKNR 643
            MNSIEDSNHVIPLLAEVGLYDCTGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAGNKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHEIGTVAWDTIGKNLLFCYQSTNEYMNGEQIVPAIEDTFVDCCEISKMISAVLCKNR
Sbjct:    1 MNSIEDSNHVIPLLAEVGLYDCTGSSSWEIEDDHVITRIYGPEGVKQSKENVQQAILDVEIHSEAGNKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQVEIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHEIGTVAWDTIGKNLLFCYQSTNEYMNGEQIVPAIEDTFVDCCEISKMISAVLCKNR 201
The following BLAST results are available for this feature:
BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 1
Match NameE-valueIdentityDescription
EXOSC54.242e-727.14exosome component 5 [Source:HGNC Symbol;Acc:HGNC:2... [more]
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
exosc53.184e-626.21exosome component 5 [Source:ZFIN;Acc:ZDB-GENE-0605... [more]
exosc53.184e-626.21exosome component 5 [Source:ZFIN;Acc:ZDB-GENE-0605... [more]
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
EXOSC53.095e-828.15exosome component 5 [Source:NCBI gene;Acc:10017061... [more]
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Exosc55.789e-727.20exosome component 5 [Source:MGI Symbol;Acc:MGI:107... [more]
Exosc55.789e-727.20exosome component 5 [Source:MGI Symbol;Acc:MGI:107... [more]
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 3
Match NameE-valueIdentityDescription
sp|O42894|RRP46_SCHPO7.892e-830.00Exosome complex component rrp46 OS=Schizosaccharom... [more]
sp|Q9NQT4|EXOS5_HUMAN2.037e-627.14Exosome complex component RRP46 OS=Homo sapiens OX... [more]
sp|Q9CRA8|EXOS5_MOUSE4.050e-627.20Exosome complex component RRP46 OS=Mus musculus OX... [more]
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0R3U5E52.430e-1332.37RNase_PH domain-containing protein OS=Mesocestoide... [more]
A0A0R3WNI68.139e-1332.31RNase_PH domain-containing protein OS=Hydatigena t... [more]
A0A0R3SBX48.460e-1333.33RNase_PH domain-containing protein OS=Hymenolepis ... [more]
A0A5J4NLI11.301e-1231.34Uncharacterized protein OS=Paragonimus westermani ... [more]
A0A0R3WBN11.936e-1231.67RNase_PH domain-containing protein OS=Taenia asiat... [more]
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
SKI67.239e-724.07Exosome non-catalytic core component; involved in ... [more]
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 2
Match NameE-valueIdentityDescription
EDO430132.400e-1025.30Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO424914.003e-626.95Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
exosc59.384e-824.39exosome component 5 [Source:NCBI gene;Acc:10116126... [more]
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BLAST of U4/U6 small nuclear ribonucleoprotein Prp4 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000026944.13.901e-149100.00SMESG000026944.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011408 ID=SMED30011408|Name=U4/U6 small nuclear ribonucleoprotein Prp4|organism=Schmidtea mediterranea sexual|type=transcript|length=786bp
TTTTTTTGTTTAAATATTGCCATATGATTTAAAATTTTGAATGAATTCAA
TTGAAGATTCAAATCACGTTATTCCATTATTGGCCGAAGTTGGTTTATAT
GACTGTACTGGTTCTTCATCTTGGGAAATAGAAGATGATCATGTAATTAC
TCGAATATATGGTCCTGAAGGTGTGAAGCAGTCAAAAGAAAATGTCCAAC
AAGCCATTTTAGACGTTGAAATTCATTCTGAGGCAGGCAATAAGAATAAG
GATGCTTTATTGCAATCTTATATTAAAAAGACTTTTGAAAAAATTCTTCA
CCTTTCTAAATACCCAAAAACAATTATCAGAATTCAAGTTGAAATAGTTT
CTGGAAAAACGGATTCTCCCACAACAATTACGGCGATTTTTAACTCAGTC
TCGTTAGCATTGTTGAATGCAGATTTTGGAATGAAATGCAGCTTATCAGC
TAGCACAGTTAGCGTTGATGGCCACGAAATTGGCACTGTAGCATGGGACA
CCATCGGCAAGAATTTGCTGTTTTGTTATCAATCCACCAATGAATATATG
AATGGCGAACAAATTGTCCCAGCTATAGAGGATACTTTCGTGGATTGTTG
TGAGATATCGAAAATGATTTCAGCGGTTTTGTGCAAGAATAGAATTTGAT
TTTTTATTTTGATTATCTAAAGCACCGCAATTATTTGAAATTTTTTTTTG
AAGCTCATTGAAAATTCTTGGTGAAATCTTTGTTAATGTTAGACTGTGAT
TTATGTTTTAAATTTTAGTATATTGAGGTTTAAAAA
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protein sequence of SMED30011408-orf-1

>SMED30011408-orf-1 ID=SMED30011408-orf-1|Name=SMED30011408-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=203bp
MNSIEDSNHVIPLLAEVGLYDCTGSSSWEIEDDHVITRIYGPEGVKQSKE
NVQQAILDVEIHSEAGNKNKDALLQSYIKKTFEKILHLSKYPKTIIRIQV
EIVSGKTDSPTTITAIFNSVSLALLNADFGMKCSLSASTVSVDGHEIGTV
AWDTIGKNLLFCYQSTNEYMNGEQIVPAIEDTFVDCCEISKMISAVLCKN
RI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR027408PNPase/RNase_PH_dom_sf
IPR001247ExoRNase_PH_dom1
IPR020568Ribosomal_S5_D2-typ_fold
Vocabulary: molecular function
TermDefinition
GO:0004527exonuclease activity
Vocabulary: biological process
TermDefinition
GO:0090305nucleic acid phosphodiester bond hydrolysis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR027408PNPase/RNase PH domain superfamilyGENE3DG3DSA:3.30.230.70coord: 18..201
e-value: 1.2E-23
score: 85.8
IPR001247Exoribonuclease, phosphorolytic domain 1PFAMPF01138RNase_PHcoord: 19..128
e-value: 3.9E-12
score: 46.8
NoneNo IPR availablePANTHERPTHR11953EXOSOME COMPLEX COMPONENTcoord: 21..153
NoneNo IPR availablePANTHERPTHR11953:SF1EXOSOME COMPLEX COMPONENT RRP46coord: 21..153
IPR020568Ribosomal protein S5 domain 2-type foldSUPERFAMILYSSF54211Ribosomal protein S5 domain 2-likecoord: 21..128