Collagen alpha-4(VI) chain

Overview
NameCollagen alpha-4(VI) chain
Smed IDSMED30006703
Length (bp)514
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30006703

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
copulatory apparatusSMED30006703h1SMcG0020768 Contig2885GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
copulatory apparatusSMED30006703h1SMcG0020768 PL05012A1F12smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
reproductive organSMED30006703h1SMcG0020768 Contig46520uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30006703h1SMcG0020768 Contig46520newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Collagen alpha-4(VI) chain vs. TrEMBL
Match: A0A2T7PUN3 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_04128 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 2.681e-9
Identity = 37/112 (33.04%), Postives = 60/112 (53.57%), Query Frame = 2 
Query:  122 LSTTCYKDLDSAIKSILIGRFMPRCDS--KGLYFRIQCTNKLCYCYHREGYRLQMFSQVYDNS--KCKCAQLVDY--------STFNKCRKDGSFKSYWCNTSQCWCINENG 421
            ++ +C ++LDS  ++  IG F+PRCD+    LY  +QC   +CYC   +G RL  +S +   +   C+CA+  D           FN C  DG++    C  S+C+C+N +G
Sbjct:   20 IAASCQEELDSRRQNYAIGGFLPRCDAGNTALYSPLQCHGSVCYCVSSDGTRLSDYSNIPIGTPGNCECAREEDEFRKTGMRGQIFN-CAPDGTYSPTRCTGSRCFCVNRDG 130

HSP 2 Score: 56.9954 bits (136), Expect = 1.499e-6
Identity = 34/114 (29.82%), Postives = 59/114 (51.75%), Query Frame = 2 
Query:  119 PLSTTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMF--SQVYDNSKCKCAQL-VDYST-------FNKCRKDGSFKSYWCNTSQCWCINENGKIV 430
            P +  C ++ D   K+ + G+    C   G Y   +CT   C+C +R+G R+Q +  + +++ S+C+CA+   DY+        FN C +DGS+ +  C  S C C+  NG  +
Sbjct:   83 PGNCECAREEDEFRKTGMRGQIF-NCAPDGTYSPTRCTGSRCFCVNRDGTRMQEYLEANIWEASECECARAKADYAERRIRGLRFN-CERDGSYGAKQCTGSTCRCVKRNGNPI 194
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BLAST of Collagen alpha-4(VI) chain vs. TrEMBL
Match: A0A3M6URL6 (Uncharacterized protein OS=Pocillopora damicornis OX=46731 GN=pdam_00011688 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 6.861e-8
Identity = 40/134 (29.85%), Postives = 65/134 (48.51%), Query Frame = 2 
Query:  107 CGLNP-LSTTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRL----------------QMFSQVYDNSKCKCAQ----LVDYSTF-NKCRKDGSFKSYWCNTSQ--CWCINENGKIVSG 436
            C  NP  +T C +    A ++  +G F+PRC S G Y  +QC   +C+C   EG  +                     V D++ C+ AQ    +V + ++  +C++DGS++   CN S   CWC+ +NG  +SG
Sbjct:  446 CAANPSANTPCLRRQFEARRNKRLGVFVPRCLSDGRYAGVQCHGSICFCMDEEGDEVSGTRVSRHLPLNCTGTNQLPPVGDSTPCQKAQRKNSVVPFGSYLVRCKQDGSYEEVQCNGSSGFCWCVQKNGTELSG 579
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BLAST of Collagen alpha-4(VI) chain vs. TrEMBL
Match: A0A2B4RH85 (Collagen alpha-4(VI) chain OS=Stylophora pistillata OX=50429 GN=Col6a4 PE=4 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 1.287e-7
Identity = 34/123 (27.64%), Postives = 53/123 (43.09%), Query Frame = 2 
Query:  125 STTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMFSQVYDNSKCKCAQLVDYST-----------------FNKCRKDGSFKSYWCNT--SQCWCINENGKIVSG 436
             T C ++  +A K    GRF+PRC   G Y  +QC   +CYC  ++G  +        + K  C      +                    +C+ DG ++   C+   SQCWC++ NGK +SG
Sbjct:  304 ETKCQREFVAATKDTAPGRFVPRCKLDGSYADVQCRGSVCYCVDKDGNEIVGTRTPLASGKPNCTAPYKLTPCQEAYRKAIQNPKVGGYVPRCKDDGEYQGLQCSGAFSQCWCVDSNGKEISG 426
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BLAST of Collagen alpha-4(VI) chain vs. TrEMBL
Match: A0A2T7PUS9 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_04132 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 1.824e-7
Identity = 37/112 (33.04%), Postives = 57/112 (50.89%), Query Frame = 2 
Query:  122 LSTTCYKDLDSAIKSILIGRFMPRCDS--KGLYFRIQCTNKLCYCYHREGYRLQMFSQVY--DNSKCKCAQ--------LVDYSTFNKCRKDGSFKSYWCNTSQCWCINENG 421
            ++ +C ++LDS  ++  IG F+PRCD+    LY  IQC    CYC   +G  L  +S +     S C+CA+         +    FN C  DG++    C  S+C+C+  NG
Sbjct:   20 IAASCQEELDSRRQNYAIGGFLPRCDAGNSALYSPIQCRGSACYCVSSDGTMLSDYSNIPFGTPSNCECARKEYEFSKARMKGQIFN-CAPDGTYSPTRCYGSRCFCVYRNG 130
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BLAST of Collagen alpha-4(VI) chain vs. TrEMBL
Match: A0A4Y2N008 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_89944_1 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 9.868e-7
Identity = 34/122 (27.87%), Postives = 58/122 (47.54%), Query Frame = 2 
Query:  122 LSTTCYKDLDSAIKSIL---IGRFMPRCDSKGLYFRIQC--TNKLCYCYHREGYRLQMFSQVYDNSKCKCAQLVDYST------FNKCRKDGSFKSYWCNTSQCWCINENGKIVSGENVENL 454
            + T C +D    + + L   I   +P CD  G Y  +QC   N  C CY R G  +   S+  +   C C +  D +         KC ++G +++  C   +CWC+++NGK++S   V ++
Sbjct:   82 VPTACEEDRARRLNATLTESILHLIPTCDENGDYAALQCFTANDWCVCYRRNGENINTPSK--NIKACDCVRQADDAKTAGDTYVPKCDRNGFYQAKQCERDECWCVDKNGKVLSDPQVGDV 201
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BLAST of Collagen alpha-4(VI) chain vs. Ensembl Nematostella
Match: EDO40369 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S7C0])

HSP 1 Score: 48.9062 bits (115), Expect = 1.329e-7
Identity = 31/120 (25.83%), Postives = 53/120 (44.17%), Query Frame = 2 
Query:  128 TTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKL--CYCYHREGYRL---------------QMFSQVYDNSKCKCAQLVDYSTFNKCRKDGSFKSYWCNTSQ--CWCINENGKIV 430
            T C K    A++  +IG ++PRC + G Y  +QC  +   C+C   +G  +                + +      +   +  V  S   +CR DGSF+   C+ SQ  CWC+++ G  +
Sbjct:    3 TACQKAYKFAVEKNVIGGYIPRCKADGRYEEVQCEGRTHSCWCVDNQGREIIGTRTQGTLVCPHPGGVLTPCQRRYQEATSSPVPGSFAPRCRADGSFEEVQCHKSQGYCWCVDQFGNEI 122
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BLAST of Collagen alpha-4(VI) chain vs. Ensembl Nematostella
Match: EDO40371 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S7C2])

HSP 1 Score: 48.521 bits (114), Expect = 1.427e-7
Identity = 34/125 (27.20%), Postives = 55/125 (44.00%), Query Frame = 2 
Query:  128 TTCYKDLDSAIKSIL-IGRFMPRCDSKGLYFRIQCTNKL--CYCYHREGYRL-------------QMFSQVYDNSKCKC----AQLVDYSTFNKCRKDGSFKSYWCNTS--QCWCINENGKIVSG 436
            T C   ++ A+K+   + RF+PRC   G Y  +QC      C+C   +G  L              M   V    + +      +LV  +   +CR DGS+    C+ S  QCWC++ +G  ++G
Sbjct:   59 TPCRAQVEQALKTPASLDRFVPRCTLDGAYEDVQCQESTGECWCVDAQGSELDGTRSTELVTCHKHMSPSVCQQDRMQALAWSGRLVVGAFIPRCRSDGSYDPIQCHESPGQCWCVDVHGNELTG 183
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BLAST of Collagen alpha-4(VI) chain vs. Ensembl Nematostella
Match: EDO40366 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S7B7])

HSP 1 Score: 45.8246 bits (107), Expect = 1.397e-6
Identity = 30/125 (24.00%), Postives = 55/125 (44.00%), Query Frame = 2 
Query:  176 GRFMPRCDSKGLYFRIQC--TNKLCYCYHREGYRLQMFSQVYDNSKCKCAQ------------LVDYSTFNK----CRKDGSFKSYWCN--TSQCWCINENGKIVSGENVENLEGFNQNKCQLNK 490
            G F+P C   G Y  +QC     LC+C  R G+ + + ++V  +  C+ AQ             + ++        C++DGSF S  C+  +++CWC++  G  + G   +      +  C   +
Sbjct:    1 GLFVPECKPDGTYEGMQCHVGTGLCWCVDRWGHEI-IGTRVKGSPDCRSAQAGLTMCQKERQIAIGWTGVAAPGSFCKQDGSFDSIQCHALSAECWCVDRRGTEIPGTRTKGRPNCEKPACMQER 124
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BLAST of Collagen alpha-4(VI) chain vs. Ensembl Nematostella
Match: EDO39095 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SB04])

HSP 1 Score: 43.1282 bits (100), Expect = 9.138e-6
Identity = 28/98 (28.57%), Postives = 42/98 (42.86%), Query Frame = 2 
Query:  173 IGRFMPRCDSKGLYFRIQCTNKL--CYCYHREGYRLQMFSQVYDNSKCKCAQLVDYST--------------FNKCRKDGSFKSYWCN--TSQCWCIN 412
            +GRF+P CD KG Y +IQC   +  C+C    G  ++  ++V     C        S                 +C KDG + +  C+  T  CWC+N
Sbjct:   79 VGRFLPSCDVKGAYEKIQCWGSIGFCWCVDSSGNEIK-GTRVRGTPSCDTTPAPTASGKHWAQSRGPLIGAYIPQCDKDGRYSALQCHGSTGYCWCVN 175
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BLAST of Collagen alpha-4(VI) chain vs. Ensembl Medaka
Match: ENSORLT00000046650.1 (pep primary_assembly:ASM223467v1:16:31876438:31883319:-1 gene:ENSORLG00000030206.1 transcript:ENSORLT00000046650.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 49.6766 bits (117), Expect = 1.060e-7
Identity = 31/123 (25.20%), Postives = 51/123 (41.46%), Query Frame = 2 
Query:  128 TTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCT-NKLCYCYHREGYRLQMFSQVYDNSKCK------CAQLVDYSTFNKCRKDGSFKSYWCNTSQCWCINENGKIVSGENVENLEGFNQNK 475
            + C ++  +A+++  +  F+P C+  G Y   QC     C+C    G  +    Q+     C        A +       +C  DGSF    C+ + CWC+ E G+ V G     L G   +K
Sbjct:   41 SPCEEERRAALETSSV--FVPTCERGGSYSFTQCQQGGQCWCVDPSGREVPGTRQLGGPLACGEKNHPLIANMAAGLQRRQCGPDGSFAPLQCDVTSCWCVTEYGQEVVGTRTPQLTGVTPSK 161
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BLAST of Collagen alpha-4(VI) chain vs. Planmine SMEST
Match: SMESG000017157.1 (SMESG000017157.1)

HSP 1 Score: 321.242 bits (822), Expect = 3.776e-114
Identity = 157/158 (99.37%), Postives = 157/158 (99.37%), Query Frame = 2 
Query:   17 FSFLVLFIGCSKGCEESSDCKQPLVCVEGICGLNPLSTTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMFSQVYDNSKCKCAQLVDYSTFNKCRKDGSFKSYWCNTSQCWCINENGKIVSGENVENLEGFNQNKCQLNK 490
             SFLVLFIGCSKGCEESSDCKQPLVCVEGICGLNPLSTTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMFSQVYDNSKCKCAQLVDYSTFNKCRKDGSFKSYWCNTSQCWCINENGKIVSGENVENLEGFNQNKCQLNK
Sbjct:    6 LSFLVLFIGCSKGCEESSDCKQPLVCVEGICGLNPLSTTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMFSQVYDNSKCKCAQLVDYSTFNKCRKDGSFKSYWCNTSQCWCINENGKIVSGENVENLEGFNQNKCQLNK 163
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BLAST of Collagen alpha-4(VI) chain vs. Planmine SMEST
Match: SMESG000017161.1 (SMESG000017161.1)

HSP 1 Score: 99.3673 bits (246), Expect = 9.506e-27
Identity = 54/159 (33.96%), Postives = 85/159 (53.46%), Query Frame = 2 
Query:   23 FLVLFIGCSKGCEESSDCKQPLVCVEGICGLNPLSTTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMFSQVYDNSKCKCAQLVDYSTFN-------KCRKDGSFKSYWCNTSQCWCINENGKIVSGENVENLEGFNQNKC 478
            FL L I  + GC +S  C    VCV G C  NPL+T CY++ D  +K++L G F+P C + G+Y  +QC   +CYC   +G ++  +  + +NS CKC       + N        C ++GS++   C  S C+C++  GK + G    ++E  N+ KC
Sbjct:    9 FLAL-IHAAFGCNDSKGCTDLEVCVSGNCSKNPLTTKCYQEYDKVMKNLLFGSFIPCCKTNGIYCPVQCPTNICYCSSPDGKKISNYFNINENSNCKCGLDKYLYSLNMAVGIIFNCNENGSYRPIQCLGSSCYCVDAQGKKIPGTISVHIEKANELKC 166
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BLAST of Collagen alpha-4(VI) chain vs. Planmine SMEST
Match: SMESG000017039.1 (SMESG000017039.1)

HSP 1 Score: 98.9821 bits (245), Expect = 1.481e-26
Identity = 52/157 (33.12%), Postives = 84/157 (53.50%), Query Frame = 2 
Query:   11 RLFSFLVLFIGCSKGCEESSDCKQPLVCVEGICGLNPLSTTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMFSQVYDNSKCKCAQL-VDYS-------TFNKCRKDGSFKSYWCNTSQCWCINENGKIVSGENVENLE 457
            R     +L +  ++GCE+S DC+ P VC+ G C  NPL+T C++    AIKS +    +PRCDS G Y  +QC N  C+C +R+G  +  +      S CKCA+  +++        T   C+ DG++    C  + C+C +E+G  + G+   + E
Sbjct:    4 RPICVFILLVEATRGCEDSFDCRPPKVCMSGKCYANPLTTKCFQIYGKAIKS-MADTLIPRCDSNGNYAPVQCQNGKCWCSNRDGITIHDYPDAKKKSHCKCARASIEFKQNSDGPITAFFCKTDGNYGDVQCKQTTCFCTDEDGVRMPGKATVDYE 159
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BLAST of Collagen alpha-4(VI) chain vs. Planmine SMEST
Match: SMESG000016977.1 (SMESG000016977.1)

HSP 1 Score: 98.2117 bits (243), Expect = 2.888e-26
Identity = 54/143 (37.76%), Postives = 79/143 (55.24%), Query Frame = 2 
Query:   56 CEESSDCKQPLVCVEGICGLNPLSTTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMFS---QVYDNSKCKCA-QLVDY------STFNKCRKDGSFKSYWCNTSQCWCINENGKIVSGENVENL 454
            C++SSDC   L+C+   C  NPL+T C+  L  A K  L+G  +P+CDS G +  +QCT   CYC  REG  ++ ++     + N  CKCA +  DY           C  +GS+ S  CN S C+C + NGK V+G+ + N+
Sbjct:   13 CQDSSDCNNDLICIGNECSDNPLNTQCFNKLSKARKGGLLGAPIPKCDSNGDFLPVQCTGSKCYCVDREGNNIRNYAAHINEFANMDCKCAREQNDYFLTGLIGKMFSCTTNGSYSSVQCNGSVCFCADYNGKAVAGKPIVNI 155
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BLAST of Collagen alpha-4(VI) chain vs. Planmine SMEST
Match: SMESG000016977.1 (SMESG000016977.1)

HSP 1 Score: 98.5969 bits (244), Expect = 3.085e-26
Identity = 55/152 (36.18%), Postives = 81/152 (53.29%), Query Frame = 2 
Query:   56 CEESSDCKQPLVCVEGICGLNPLSTTCYKDLDSAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMFS---QVYDNSKCKCA-QLVDY------STFNKCRKDGSFKSYWCNTSQCWCINENGKIVSGENVENLEGFNQNKCQ 481
            C++SSDC   L+C+   C  NPL+T C+  L  A K  L+G  +P+CDS G +  +QCT   CYC  REG  ++ ++     + N  CKCA +  DY           C  +GS+ S  CN S C+C + NGK V+G+ + N+      +C 
Sbjct:   24 CQDSSDCNNDLICIGNECSDNPLNTQCFNKLSKARKGGLLGAPIPKCDSNGDFLPVQCTGSKCYCVDREGNNIRNYAAHINEFANMDCKCAREQNDYFLTGLIGKMFSCTTNGSYSSVQCNGSVCFCADYNGKAVAGKPIVNIGQIQSLRCN 175
The following BLAST results are available for this feature:
BLAST of Collagen alpha-4(VI) chain vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Collagen alpha-4(VI) chain 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 Collagen alpha-4(VI) chain 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 Collagen alpha-4(VI) chain vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Collagen alpha-4(VI) chain vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Collagen alpha-4(VI) chain vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Collagen alpha-4(VI) chain vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Collagen alpha-4(VI) chain vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2T7PUN32.681e-933.04Uncharacterized protein OS=Pomacea canaliculata OX... [more]
A0A3M6URL66.861e-829.85Uncharacterized protein OS=Pocillopora damicornis ... [more]
A0A2B4RH851.287e-727.64Collagen alpha-4(VI) chain OS=Stylophora pistillat... [more]
A0A2T7PUS91.824e-733.04Uncharacterized protein OS=Pomacea canaliculata OX... [more]
A0A4Y2N0089.868e-727.87Uncharacterized protein OS=Araneus ventricosus OX=... [more]
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BLAST of Collagen alpha-4(VI) chain 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 Collagen alpha-4(VI) chain 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 Collagen alpha-4(VI) chain vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Collagen alpha-4(VI) chain vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 4
Match NameE-valueIdentityDescription
EDO403691.329e-725.83Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO403711.427e-727.20Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO403661.397e-624.00Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO390959.138e-628.57Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of Collagen alpha-4(VI) chain vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSORLT00000046650.11.060e-725.20pep primary_assembly:ASM223467v1:16:31876438:31883... [more]
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BLAST of Collagen alpha-4(VI) chain vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000017157.13.776e-11499.37SMESG000017157.1[more]
SMESG000017161.19.506e-2733.96SMESG000017161.1[more]
SMESG000017039.11.481e-2633.12SMESG000017039.1[more]
SMESG000016977.12.888e-2637.76SMESG000016977.1[more]
SMESG000016977.13.085e-2636.18SMESG000016977.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006703 ID=SMED30006703|Name=Collagen alpha-4(VI) chain|organism=Schmidtea mediterranea sexual|type=transcript|length=514bp
TCCGATCTCTAGATTATTTAGTTTTTTAGTGCTATTTATTGGATGCTCCA
AGGGTTGTGAGGAATCCTCTGACTGTAAGCAGCCTCTGGTTTGCGTGGAG
GGCATTTGTGGACTGAATCCGCTTTCCACAACATGTTATAAGGACCTTGA
CAGTGCGATTAAAAGTATATTAATTGGTCGTTTTATGCCTAGATGTGATT
CTAAAGGACTTTATTTCCGTATCCAATGCACGAACAAACTATGTTATTGC
TACCACCGTGAAGGATACAGACTTCAAATGTTTTCTCAAGTCTACGACAA
TTCCAAATGCAAATGCGCCCAACTAGTGGACTATTCTACGTTTAACAAAT
GTCGCAAGGATGGAAGCTTTAAATCATATTGGTGTAATACGTCGCAATGT
TGGTGTATTAATGAAAATGGGAAGATTGTTTCTGGAGAAAATGTTGAAAA
CCTTGAAGGTTTCAATCAAAATAAATGCCAGTTGAATAAATAAATGTTTT
CTTTTGAAAAAAAA
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protein sequence of SMED30006703-orf-1

>SMED30006703-orf-1 ID=SMED30006703-orf-1|Name=SMED30006703-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=164bp
PISRLFSFLVLFIGCSKGCEESSDCKQPLVCVEGICGLNPLSTTCYKDLD
SAIKSILIGRFMPRCDSKGLYFRIQCTNKLCYCYHREGYRLQMFSQVYDN
SKCKCAQLVDYSTFNKCRKDGSFKSYWCNTSQCWCINENGKIVSGENVEN
LEGFNQNKCQLNK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0005576extracellular region
GO:0005581collagen trimer
Vocabulary: biological process
TermDefinition
GO:0010466negative regulation of peptidase activity
Vocabulary: molecular function
TermDefinition
GO:0030414peptidase inhibitor activity
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000232copulatory apparatus
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR036857Thyroglobulin_1_sf
IPR000716Thyroglobulin_1
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000716Thyroglobulin type-1SMARTSM00211TY_2coord: 60..107
e-value: 0.024
score: 19.0
coord: 114..161
e-value: 0.37
score: 8.5
IPR000716Thyroglobulin type-1PFAMPF00086Thyroglobulin_1coord: 114..147
e-value: 3.9E-6
score: 26.4
coord: 56..101
e-value: 7.5E-7
score: 28.7
IPR000716Thyroglobulin type-1PROSITEPS51162THYROGLOBULIN_1_2coord: 40..157
score: 8.51
IPR036857Thyroglobulin type-1 superfamilyGENE3DG3DSA:4.10.800.10coord: 40..104
e-value: 2.4E-9
score: 38.4
IPR036857Thyroglobulin type-1 superfamilySUPERFAMILYSSF57610Thyroglobulin type-1 domaincoord: 114..146
IPR036857Thyroglobulin type-1 superfamilySUPERFAMILYSSF57610Thyroglobulin type-1 domaincoord: 43..103
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.646