SMED30017415

Overview
NameSMED30017415
Smed IDSMED30017415
Length (bp)991
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 SMED30017415 (SMED30017415) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017415 (SMED30017415) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30017415 (SMED30017415) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017415 (SMED30017415) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30017415

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
nervous systemSMED30017415SMESG000002106.1 SMESG000002091.1 dd_Smed_v4_2453_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30017415SMESG000002106.1 SMESG000002091.1 dd_Smed_v4_2453_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30017415SMESG000002106.1 SMESG000002091.1 dd_Smed_v4_2453_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30017415SMESG000002106.1 SMESG000002091.1 dd_Smed_v4_2453_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017415SMESG000002106.1 SMESG000002091.1 Contig25175newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017415SMESG000002106.1 SMESG000002091.1 Contig25175uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30017415SMESG000002106.1 SMESG000002091.1 dd_Smed_v4_2453_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017415 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003918:5217..6314 +4540
v31.000333:13299..14273 +4350
Homology
[Close]
BLAST of SMED30017415 vs. Ensembl Zebrafish
Match: mib2 (mindbomb E3 ubiquitin protein ligase 2 [Source:ZFIN;Acc:ZDB-GENE-050628-1])

HSP 1 Score: 50.0618 bits (118), Expect = 2.810e-6
Identity = 21/45 (46.67%), Postives = 26/45 (57.78%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN + +V QCGH  C  CS  L  C  C   I+ RIQL
Sbjct:  843 ITCPICIDNHIRLVFQCGHASCIDCSSALKTCPICRQTIRERIQL 887

HSP 2 Score: 48.521 bits (114), Expect = 7.482e-6
Identity = 38/129 (29.46%), Postives = 60/129 (46.51%), Query Frame = 1 
Query:  436 VNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTAL------TQLLEKIS------------ICTN---ANSNRKLISAIKS-IVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRK 756
            +N++N RNQT LQ+A+    M L+  L+ E    ++ED+DG TA+       QL   IS            +C++    N+   + +AI   + Q G DI      GK  +D   D +V+  +  F  K
Sbjct:  594 INIRNNRNQTPLQLAVTQGHMALVALLVMEGADVNAEDEDGDTAMHTSLSRQQLTTVISSAEGDGAVLYGRLCSSGLMGNTELNVGAAIACFLAQEGADISYANHKGKSPLDLVTDSSVQTLIRSFAEK 722
[Close]
BLAST of SMED30017415 vs. Ensembl Xenopus
Match: coa7 (cytochrome c oxidase assembly factor 7 (putative) [Source:Xenbase;Acc:XB-GENE-6258829])

HSP 1 Score: 49.6766 bits (117), Expect = 5.246e-6
Identity = 20/45 (44.44%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQ+
Sbjct:  902 ITCPICIDNHIKLVFQCGHGSCTECSTSLTACPICRQLIRERIQI 946
[Close]
BLAST of SMED30017415 vs. Ensembl Xenopus
Match: coa7 (cytochrome c oxidase assembly factor 7 (putative) [Source:Xenbase;Acc:XB-GENE-6258829])

HSP 1 Score: 49.6766 bits (117), Expect = 5.250e-6
Identity = 20/45 (44.44%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQ+
Sbjct:  905 ITCPICIDNHIKLVFQCGHGSCTECSTSLTACPICRQLIRERIQI 949
[Close]
BLAST of SMED30017415 vs. Ensembl Xenopus
Match: coa7 (cytochrome c oxidase assembly factor 7 (putative) [Source:Xenbase;Acc:XB-GENE-6258829])

HSP 1 Score: 49.6766 bits (117), Expect = 5.308e-6
Identity = 20/45 (44.44%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQ+
Sbjct:  915 ITCPICIDNHIKLVFQCGHGSCTECSTSLTACPICRQLIRERIQI 959
[Close]
BLAST of SMED30017415 vs. Ensembl Xenopus
Match: coa7 (cytochrome c oxidase assembly factor 7 (putative) [Source:Xenbase;Acc:XB-GENE-6258829])

HSP 1 Score: 49.2914 bits (116), Expect = 7.087e-6
Identity = 20/45 (44.44%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQ+
Sbjct:  906 ITCPICIDNHIKLVFQCGHGSCTECSTSLTACPICRQLIRERIQI 950
[Close]
BLAST of SMED30017415 vs. Ensembl Xenopus
Match: coa7 (cytochrome c oxidase assembly factor 7 (putative) [Source:Xenbase;Acc:XB-GENE-6258829])

HSP 1 Score: 48.9062 bits (115), Expect = 8.686e-6
Identity = 20/45 (44.44%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQ+
Sbjct:  870 ITCPICIDNHIKLVFQCGHGSCTECSTSLTACPICRQLIRERIQI 914
[Close]
BLAST of SMED30017415 vs. UniProt/SwissProt
Match: sp|Q9SS90|RGLG1_ARATH (E3 ubiquitin-protein ligase RGLG1 OS=Arabidopsis thaliana OX=3702 GN=RGLG1 PE=1 SV=1)

HSP 1 Score: 52.7582 bits (125), Expect = 2.426e-6
Identity = 24/58 (41.38%), Postives = 32/58 (55.17%), Query Frame = 1 
Query:  766 KSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            +SK+  + DD    +C IC+ N   +   CGH  CC C   L VC  C A I+TRI+L
Sbjct:  433 ESKQMSSADDI--QLCPICLSNPKNMAFGCGHQTCCECGPDLKVCPICRAPIQTRIKL 488
[Close]
BLAST of SMED30017415 vs. UniProt/SwissProt
Match: sp|Q9LY87|RGLG2_ARATH (E3 ubiquitin-protein ligase RGLG2 OS=Arabidopsis thaliana OX=3702 GN=RGLG2 PE=1 SV=1)

HSP 1 Score: 51.9878 bits (123), Expect = 4.379e-6
Identity = 19/44 (43.18%), Postives = 26/44 (59.09%), Query Frame = 1 
Query:  808 ICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            +C IC+ N  ++   CGH  CC C   L +C  C A I+TRI+L
Sbjct:  424 LCPICLSNPKDMAFGCGHQTCCECGPDLQMCPICRAPIQTRIKL 467
[Close]
BLAST of SMED30017415 vs. Ensembl Cavefish
Match: mib2 (mindbomb E3 ubiquitin protein ligase 2 [Source:NCBI gene;Acc:103034310])

HSP 1 Score: 51.2174 bits (121), Expect = 9.958e-7
Identity = 21/45 (46.67%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQL
Sbjct:  971 ITCPICIDNQIKLVFQCGHASCIDCSAALKTCPICRQTIRERIQL 1015
[Close]
BLAST of SMED30017415 vs. Ensembl Cavefish
Match: mib2 (mindbomb E3 ubiquitin protein ligase 2 [Source:NCBI gene;Acc:103034310])

HSP 1 Score: 51.2174 bits (121), Expect = 1.030e-6
Identity = 21/45 (46.67%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQL
Sbjct:  965 ITCPICIDNQIKLVFQCGHASCIDCSAALKTCPICRQTIRERIQL 1009
[Close]
BLAST of SMED30017415 vs. Ensembl Cavefish
Match: mib2 (mindbomb E3 ubiquitin protein ligase 2 [Source:NCBI gene;Acc:103034310])

HSP 1 Score: 50.447 bits (119), Expect = 1.638e-6
Identity = 21/45 (46.67%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQL
Sbjct:  901 ITCPICIDNQIKLVFQCGHASCIDCSAALKTCPICRQTIRERIQL 945
[Close]
BLAST of SMED30017415 vs. Ensembl Medaka
Match: mib2 (mindbomb E3 ubiquitin protein ligase 2 [Source:NCBI gene;Acc:101175479])

HSP 1 Score: 52.373 bits (124), Expect = 4.853e-7
Identity = 21/45 (46.67%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQL
Sbjct: 1038 ITCPICIDNHIKLVFQCGHASCIECSAALKTCPICRQTIRERIQL 1082
[Close]
BLAST of SMED30017415 vs. Ensembl Medaka
Match: mib2 (mindbomb E3 ubiquitin protein ligase 2 [Source:NCBI gene;Acc:101175479])

HSP 1 Score: 51.9878 bits (123), Expect = 6.208e-7
Identity = 21/45 (46.67%), Postives = 27/45 (60.00%), Query Frame = 1 
Query:  805 MICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            + C IC+DN +++V QCGH  C  CS  L  C  C   I+ RIQL
Sbjct:  982 ITCPICIDNHIKLVFQCGHASCIECSAALKTCPICRQTIRERIQL 1026
[Close]
BLAST of SMED30017415 vs. Planmine SMEST
Match: SMESG000002106.1 (SMESG000002106.1)

HSP 1 Score: 637.106 bits (1642), Expect = 0.000e+0
Identity = 313/313 (100.00%), Postives = 313/313 (100.00%), Query Frame = 1 
Query:    1 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL
Sbjct:  552 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 864
[Close]
BLAST of SMED30017415 vs. Planmine SMEST
Match: SMESG000002106.1 (SMESG000002106.1)

HSP 1 Score: 637.106 bits (1642), Expect = 0.000e+0
Identity = 313/313 (100.00%), Postives = 313/313 (100.00%), Query Frame = 1 
Query:    1 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL
Sbjct:  543 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 855
[Close]
BLAST of SMED30017415 vs. Planmine SMEST
Match: SMESG000002106.1 (SMESG000002106.1)

HSP 1 Score: 637.106 bits (1642), Expect = 0.000e+0
Identity = 313/313 (100.00%), Postives = 313/313 (100.00%), Query Frame = 1 
Query:    1 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL
Sbjct:  581 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 893
[Close]
BLAST of SMED30017415 vs. Planmine SMEST
Match: SMESG000002106.1 (SMESG000002106.1)

HSP 1 Score: 636.721 bits (1641), Expect = 0.000e+0
Identity = 313/313 (100.00%), Postives = 313/313 (100.00%), Query Frame = 1 
Query:    1 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL
Sbjct:  580 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 892
[Close]
BLAST of SMED30017415 vs. Planmine SMEST
Match: SMESG000002091.1 (SMESG000002091.1)

HSP 1 Score: 608.601 bits (1568), Expect = 0.000e+0
Identity = 302/313 (96.49%), Postives = 302/313 (96.49%), Query Frame = 1 
Query:    1 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFNRKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEIKTRIQL 939
            GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVK DVIEFNRKILTKSKK      K   ICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEI TRIQL
Sbjct:  319 GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSSNITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIFDHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKNKRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISICTNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKTDVIEFNRKILTKSKKLV----KKRPICNICMDNLVEIVLQCGHLLCCRCSDQLFVCHACNAEITTRIQL 627
The following BLAST results are available for this feature:
BLAST of SMED30017415 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017415 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017415 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017415 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
mib22.810e-646.67mindbomb E3 ubiquitin protein ligase 2 [Source:ZFI... [more]
back to top
BLAST of SMED30017415 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 5
Match NameE-valueIdentityDescription
coa75.246e-644.44cytochrome c oxidase assembly factor 7 (putative) ... [more]
coa75.250e-644.44cytochrome c oxidase assembly factor 7 (putative) ... [more]
coa75.308e-644.44cytochrome c oxidase assembly factor 7 (putative) ... [more]
coa77.087e-644.44cytochrome c oxidase assembly factor 7 (putative) ... [more]
coa78.686e-644.44cytochrome c oxidase assembly factor 7 (putative) ... [more]
back to top
BLAST of SMED30017415 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017415 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 2
Match NameE-valueIdentityDescription
sp|Q9SS90|RGLG1_ARATH2.426e-641.38E3 ubiquitin-protein ligase RGLG1 OS=Arabidopsis t... [more]
sp|Q9LY87|RGLG2_ARATH4.379e-643.18E3 ubiquitin-protein ligase RGLG2 OS=Arabidopsis t... [more]
back to top
BLAST of SMED30017415 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017415 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 3
Match NameE-valueIdentityDescription
mib29.958e-746.67mindbomb E3 ubiquitin protein ligase 2 [Source:NCB... [more]
mib21.030e-646.67mindbomb E3 ubiquitin protein ligase 2 [Source:NCB... [more]
mib21.638e-646.67mindbomb E3 ubiquitin protein ligase 2 [Source:NCB... [more]
back to top
BLAST of SMED30017415 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017415 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017415 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017415 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 2
Match NameE-valueIdentityDescription
mib24.853e-746.67mindbomb E3 ubiquitin protein ligase 2 [Source:NCB... [more]
mib26.208e-746.67mindbomb E3 ubiquitin protein ligase 2 [Source:NCB... [more]
back to top
BLAST of SMED30017415 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000002106.10.000e+0100.00SMESG000002106.1[more]
SMESG000002106.10.000e+0100.00SMESG000002106.1[more]
SMESG000002106.10.000e+0100.00SMESG000002106.1[more]
SMESG000002106.10.000e+0100.00SMESG000002106.1[more]
SMESG000002091.10.000e+096.49SMESG000002091.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017415 ID=SMED30017415|Name=SMED30017415|organism=Schmidtea mediterranea sexual|type=transcript|length=991bp
GGCAGTGAAAGATTAATGCTTGCCCTTGTATCGAATAATCCAATGTTGAG
AAATTTCTCTTCCGATGATTTCCAATTAGCTTTCAGCAATCAGTGGCACA
AATATGGTGAAACGTTGATCAAGATTTTACCAGACAATTTTCTATCTTCA
AATATCACAATTGAAACATTTCAATCATCAAAGAAAGCCGAACCAAAATT
AATAAAGATTCTTTTCGACAAATCCAGTCCCGAATTGCAGCAATCAATTT
TGGAAAATTTTCTTTATGAAGCTTCTAATAACGATGGCAACGAGATCTTT
GACCACATGATTAACATAGAAATATTGCAACCAAGTGAACTCAGAAACGG
AGAGACGCTGCTGACTGCTTTGATGAAAGAAAATAAAATTGGATTTGTGT
GGAAACTTTTAGATTCGATAAATAAAACAAAATTTGTCAATGTGAAAAAC
AAAAGAAATCAAACTGCTCTCCAAGTGGCCATTGAAATTGAGGAAATGGA
TCTGATTGACAATTTAATTTATGAATCAGAAGGATTCGACAGTGAAGATA
AAGATGGAAGGACGGCATTAACACAATTATTGGAGAAAATATCAATTTGC
ACAAATGCAAATTCCAACAGGAAATTGATCTCAGCTATTAAATCTATCGT
CCAAGCCGGGGGTGACATTTATATGGTGACCTCTCTCGGTAAGCAGGTGA
TTGACGCGTGCGCAGATGGCAATGTCAAGGCAGATGTTATAGAATTTAAC
AGAAAGATTCTCACAAAATCAAAAAAAGAAAAGAATGACGATGATAAGGG
GAGCATGATATGTAACATATGCATGGATAATCTTGTGGAAATTGTGCTGC
AATGTGGGCATTTGCTCTGCTGTCGTTGTTCTGATCAGCTGTTTGTTTGC
CATGCTTGTAACGCCGAGATCAAAACTCGTATACAACTTTATTTCAACTG
ATTTTATCAATTTATATTTTATTTTGTTGCTTGTCTGACAG
back to top

protein sequence of SMED30017415-orf-1

>SMED30017415-orf-1 ID=SMED30017415-orf-1|Name=SMED30017415-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=317bp
GSERLMLALVSNNPMLRNFSSDDFQLAFSNQWHKYGETLIKILPDNFLSS
NITIETFQSSKKAEPKLIKILFDKSSPELQQSILENFLYEASNNDGNEIF
DHMINIEILQPSELRNGETLLTALMKENKIGFVWKLLDSINKTKFVNVKN
KRNQTALQVAIEIEEMDLIDNLIYESEGFDSEDKDGRTALTQLLEKISIC
TNANSNRKLISAIKSIVQAGGDIYMVTSLGKQVIDACADGNVKADVIEFN
RKILTKSKKEKNDDDKGSMICNICMDNLVEIVLQCGHLLCCRCSDQLFVC
HACNAEIKTRIQLYFN*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR036770Ankyrin_rpt-contain_sf
IPR013083Znf_RING/FYVE/PHD
IPR020683Ankyrin_rpt-contain_dom
IPR001841Znf_RING
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0005515protein binding
GO:0004842ubiquitin-protein transferase activity
GO:0016740transferase activity
GO:0046872metal ion binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005886plasma membrane
GO:0016020membrane
Vocabulary: biological process
TermDefinition
GO:0009738abscisic acid-activated signaling pathway
GO:0016567protein ubiquitination
GO:0080148negative regulation of response to water deprivation
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036770Ankyrin repeat-containing domain superfamilyGENE3DG3DSA:1.25.40.20coord: 63..245
e-value: 1.8E-8
score: 36.0
IPR036770Ankyrin repeat-containing domain superfamilySUPERFAMILYSSF48403Ankyrin repeatcoord: 85..238
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 246..313
e-value: 9.6E-11
score: 43.0
IPR020683Ankyrin repeat-containing domainPROSITEPS50297ANK_REP_REGIONcoord: 143..187
score: 9.49
IPR001841Zinc finger, RING-typePROSITEPS50089ZF_RING_2coord: 268..301
score: 9.863
NoneNo IPR availableSUPERFAMILYSSF57850RING/U-boxcoord: 261..306