SRR1 domain-containing protein

Overview
NameSRR1 domain-containing protein
Smed IDSMED30001487
Length (bp)911
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 SRR1 domain-containing protein (SMED30001487) t-SNE clustered cells

Violin plots show distribution of expression levels for SRR1 domain-containing protein (SMED30001487) 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 SRR1 domain-containing protein (SMED30001487) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SRR1 domain-containing protein (SMED30001487) 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



SMED30001487

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30001487SMESG000055065.1 SmedASXL_006210SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SRR1 domain-containing protein vs. Ensembl Mouse
Match: Srrd (SRR1 domain containing [Source:MGI Symbol;Acc:MGI:1917368])

HSP 1 Score: 47.7506 bits (112), Expect = 6.463e-6
Identity = 27/88 (30.68%), Postives = 42/88 (47.73%), Query Frame = 1 
Query:  322 IDLFCYGLGNPSNSKDSLYQLALLVLMCEEFSVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDSPINKCSFIF-MPHCPHFL 582
            +   CYGLG  ++   +  QLA ++L  E+  V   S  +VYDP+ S+  +  +  L   + S N  G   +     +F MPHC   L
Sbjct:  108 VKCVCYGLGTFASCPTARIQLAFMLLFLEKCQVPR-SHCWVYDPLFSQTEVSVLTSLGVTVLSENEEGKRSVQGQPTVFYMPHCGTAL 194
[Close]
BLAST of SRR1 domain-containing protein vs. TrEMBL
Match: A0A0R3U4V6 (SRR1 domain-containing protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS1703 PE=4 SV=1)

HSP 1 Score: 82.0333 bits (201), Expect = 3.262e-14
Identity = 49/146 (33.56%), Postives = 76/146 (52.05%), Query Frame = 1 
Query:  169 SDKKP---IYIPDDNIGEIRKKFVNVTALLRNSKFWWNLKIDLKYILTFFDQISIDLFCYGLGNPSNSKDSLYQLALLVLMCEEF-SVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDS--PINKCSFIFMPHCPHFLVK 588
            S+KKP   +Y+PDD+   ++ KF    A    S+   +    +   L    + S  + C GLGNP+    SL QLA L  + E    +F  ++TF+YDP+L   S +FI+   F + S N  G    P ++ +F+F+PHCP  L +
Sbjct:   55 SEKKPRTLLYLPDDSPSALKAKFGAALAQFLPSEGSASFVARVLSELRARIRPSAKILCLGLGNPAVDSSSLRQLAFLTALVEASDGIFAPARTFIYDPVLKITSRDFIRRQGFRVLSSNLEGHYHLPRDQSTFVFLPHCPLALAE 200
[Close]
BLAST of SRR1 domain-containing protein vs. TrEMBL
Match: A0A0X3PYI9 (SRR1 domain-containing protein (Fragment) OS=Schistocephalus solidus OX=70667 GN=TR148928 PE=4 SV=1)

HSP 1 Score: 74.3294 bits (181), Expect = 3.088e-11
Identity = 47/109 (43.12%), Postives = 66/109 (60.55%), Query Frame = 1 
Query:  331 FCYGLGNPSNSKDSLYQLALLVLMCEEFSVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDS--PINKCSFIFMPHCPHFLVKXXXXXXXXXXXXXXXXFYSNS 651
             C GLGNP+  + SL QLALL  + +  ++F  SKT+ YDP+L + S EFI+ L F I   N  G    P +  +  F+PHCP  L  +++ +NWS +SL  L+FYS S
Sbjct:  172 LCLGLGNPAVDRSSLRQLALLTTLVKHTALFKPSKTYFYDPLLRQTSREFIRRLGFRILCSNTEGKYVLPQSHFTLAFLPHCPPALADSLLAANWSSHSLQRLVFYSCS 280
[Close]
BLAST of SRR1 domain-containing protein vs. TrEMBL
Match: A0A0X3PGJ9 (SRR1 domain-containing protein OS=Schistocephalus solidus OX=70667 GN=TR148928 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 3.261e-11
Identity = 47/109 (43.12%), Postives = 66/109 (60.55%), Query Frame = 1 
Query:  331 FCYGLGNPSNSKDSLYQLALLVLMCEEFSVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDS--PINKCSFIFMPHCPHFLVKXXXXXXXXXXXXXXXXFYSNS 651
             C GLGNP+  + SL QLALL  + +  ++F  SKT+ YDP+L + S EFI+ L F I   N  G    P +  +  F+PHCP  L  +++ +NWS +SL  L+FYS S
Sbjct:  128 LCLGLGNPAVDRSSLRQLALLTTLVKHTALFKPSKTYFYDPLLRQTSREFIRRLGFRILCSNTEGKYVLPQSHFTLAFLPHCPPALADSLLAANWSSHSLQRLVFYSCS 236
[Close]
BLAST of SRR1 domain-containing protein vs. TrEMBL
Match: A0A068YHW7 (Protein sensitivity to red light reduced OS=Echinococcus multilocularis OX=6211 GN=EmuJ_001062200 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 4.234e-11
Identity = 52/158 (32.91%), Postives = 77/158 (48.73%), Query Frame = 1 
Query:  136 VTKKFKTIKPKSDKKPIYI-PDDNIGEIRKKF-VNVTALLRNSKFWWNLKIDLKYILTFFDQIS--IDLFCYGLGNPSNSKDSLYQLALLVLMCEEF-SVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDS--PINKCSFIFMPHCPHFLVK 588
            +T    T      ++ ++I PDD+   +  KF   + + LR +     + I L  + + F   S    L C GLGNP+    SL QLA L  + +    +F   KTFVYDP+L   S  FI++L F I S N  G    P  + + +F+PHCP  L +
Sbjct:   49 ITLPVPTNSSSCGRRTVFILPDDSPSALSSKFDAALASFLRPNSL---VSIVLAQLRSRFRCSSSFAPLLCLGLGNPAVDSASLRQLAFLAALVQTSDGIFSPGKTFVYDPVLKTTSRNFIRQLGFCILSSNLEGQYQLPRERPTLVFLPHCPIALAE 203
[Close]
BLAST of SRR1 domain-containing protein vs. TrEMBL
Match: A0A068WJI7 (Protein sensitivity to red light reduced OS=Echinococcus granulosus OX=6210 GN=EgrG_001062200 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 4.316e-11
Identity = 52/158 (32.91%), Postives = 77/158 (48.73%), Query Frame = 1 
Query:  136 VTKKFKTIKPKSDKKPIYI-PDDNIGEIRKKF-VNVTALLRNSKFWWNLKIDLKYILTFFDQIS--IDLFCYGLGNPSNSKDSLYQLALLVLMCEEF-SVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDS--PINKCSFIFMPHCPHFLVK 588
            +T    T      ++ ++I PDD+   +  KF   + + LR +     + I L  + + F   S    L C GLGNP+    SL QLA L  + +    +F   KTFVYDP+L   S  FI++L F I S N  G    P  + + +F+PHCP  L +
Sbjct:   49 ITLPVPTNSSSCGRRTVFILPDDSPSALSSKFDTALASFLRPNSL---VAIVLAQLRSRFRCSSSFAPLLCLGLGNPAVDSASLRQLAFLAALVQTSDGIFSPGKTFVYDPVLKTTSRNFIRQLGFCILSSNLEGQYQLPRERPTLVFLPHCPIALAE 203
[Close]
BLAST of SRR1 domain-containing protein vs. Ensembl Cavefish
Match: srrd (SRR1 domain containing [Source:NCBI gene;Acc:103044606])

HSP 1 Score: 57.7658 bits (138), Expect = 3.245e-9
Identity = 31/90 (34.44%), Postives = 49/90 (54.44%), Query Frame = 1 
Query:  319 SIDLFCYGLGNPSNSKDSLYQLALLVLMCE--EFSVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDSPINKCSFIFMPHCPHFL 582
             ++  CYGLGN S+   + YQLA+L+L+ E  +  V  CS   +YDP+ +    E +KEL F + + N  G   +   +F ++ HC   L
Sbjct:   86 QLECVCYGLGNFSSCVSARYQLAMLLLLFEALQIPVGQCS---MYDPVFTVTECEILKELGFTVLTENEEGKRAVCHPTFFYLMHCGKAL 172
[Close]
BLAST of SRR1 domain-containing protein vs. Planmine SMEST
Match: SMESG000055065.1 (SMESG000055065.1)

HSP 1 Score: 452.21 bits (1162), Expect = 3.319e-162
Identity = 258/259 (99.61%), Postives = 258/259 (99.61%), Query Frame = 1 
Query:  118 MEDWKIVTKKFKTIKPKSDKKPIYIPDDNIGEIRKKFVNVTALLRNSKFWWNLKIDLKYILTFFDQISIDLFCYGLGNPSNSKDSLYQLALLVLMCEEFSVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDSPINKCSFIFMPHCPHFLVKXXXXXXXXXXXXXXXXFYSNSWXXXXXXXXXXXXXXXPEDLHNFIPKIRGLMKSESVEIIQTTSYKLKSELCIYSPFENLDFHFFIRDILRSKSDANNFNAD 894
            MEDWKIVTKKFKTIKPKSDKKPIYIPDDNIGEIRKKFVNVTALLRNSKFWWNLKIDLKYILTFFDQISIDLFCYGLGNPSNSKDSLYQLALLVLMCEEFSVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDSPINKCSFIFMPHCPHFLVKNIILSNWSINSLSNLIFYSNSWE LYSELSIYESEYSPEDLHNFIPKIRGLMKSESVEIIQTTSYKLKSELCIYSPFENLDFHFFIRDILRSKSDANNFNAD
Sbjct:    1 MEDWKIVTKKFKTIKPKSDKKPIYIPDDNIGEIRKKFVNVTALLRNSKFWWNLKIDLKYILTFFDQISIDLFCYGLGNPSNSKDSLYQLALLVLMCEEFSVFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDSPINKCSFIFMPHCPHFLVKNIILSNWSINSLSNLIFYSNSWETLYSELSIYESEYSPEDLHNFIPKIRGLMKSESVEIIQTTSYKLKSELCIYSPFENLDFHFFIRDILRSKSDANNFNAD 259
The following BLAST results are available for this feature:
BLAST of SRR1 domain-containing protein 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 SRR1 domain-containing protein 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 SRR1 domain-containing protein 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 SRR1 domain-containing protein vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SRR1 domain-containing protein vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SRR1 domain-containing protein vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Srrd6.463e-630.68SRR1 domain containing [Source:MGI Symbol;Acc:MGI:... [more]
back to top
BLAST of SRR1 domain-containing protein vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SRR1 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0R3U4V63.262e-1433.56SRR1 domain-containing protein OS=Mesocestoides co... [more]
A0A0X3PYI93.088e-1143.12SRR1 domain-containing protein (Fragment) OS=Schis... [more]
A0A0X3PGJ93.261e-1143.12SRR1 domain-containing protein OS=Schistocephalus ... [more]
A0A068YHW74.234e-1132.91Protein sensitivity to red light reduced OS=Echino... [more]
A0A068WJI74.316e-1132.91Protein sensitivity to red light reduced OS=Echino... [more]
back to top
BLAST of SRR1 domain-containing protein vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
srrd3.245e-934.44SRR1 domain containing [Source:NCBI gene;Acc:10304... [more]
back to top
BLAST of SRR1 domain-containing protein 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 SRR1 domain-containing protein 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 SRR1 domain-containing protein 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 SRR1 domain-containing protein vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SRR1 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000055065.13.319e-16299.61SMESG000055065.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001487 ID=SMED30001487|Name=SRR1 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=911bp
GTTTAAATATTGATAATCTCATGCGATAGTTATTTAAAATTAATCTTTAT
TATTTATTAAGACAATTTTAATTTATCTAAAAACTTTTAAATTTTCAGTA
AAACATTTTACAAATATATGGAAGATTGGAAAATCGTTACTAAAAAATTT
AAGACAATTAAGCCTAAAAGTGATAAAAAACCTATTTATATTCCTGATGA
TAATATTGGAGAAATAAGAAAAAAATTTGTTAATGTAACTGCTCTACTAA
GAAATTCTAAATTTTGGTGGAATTTAAAAATTGATTTAAAATACATATTA
ACTTTTTTTGACCAAATATCCATTGATCTATTTTGTTATGGTTTGGGTAA
CCCTTCTAATAGCAAGGATAGTCTTTACCAATTGGCGCTTTTAGTTTTGA
TGTGTGAAGAATTTTCAGTATTTGATTGTTCCAAAACATTTGTTTACGAT
CCTATTCTGTCAGAAGTTTCAATCGAGTTCATAAAAGAATTAAATTTTGA
TATTCCATCATTTAATCACAATGGAGACAGTCCAATTAATAAATGTTCTT
TCATATTTATGCCACATTGCCCACATTTTCTTGTAAAAAATATCATTTTA
TCCAATTGGTCTATTAATAGTCTTTCCAATTTAATTTTCTATTCAAATTC
TTGGGAAATTCTTTACTCTGAATTAAGCATTTACGAATCCGAATATTCAC
CAGAAGACCTCCATAATTTTATCCCAAAAATCAGAGGCCTAATGAAATCA
GAATCTGTGGAAATCATTCAAACCACATCATACAAACTGAAATCTGAATT
GTGCATTTATTCTCCGTTTGAAAATTTGGATTTTCATTTCTTTATCCGTG
ATATTTTGCGTTCCAAATCCGATGCCAACAATTTCAATGCTGATTAATTA
TTATTTGTAGC
back to top

protein sequence of SMED30001487-orf-1

>SMED30001487-orf-1 ID=SMED30001487-orf-1|Name=SMED30001487-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=260bp
MEDWKIVTKKFKTIKPKSDKKPIYIPDDNIGEIRKKFVNVTALLRNSKFW
WNLKIDLKYILTFFDQISIDLFCYGLGNPSNSKDSLYQLALLVLMCEEFS
VFDCSKTFVYDPILSEVSIEFIKELNFDIPSFNHNGDSPINKCSFIFMPH
CPHFLVKNIILSNWSINSLSNLIFYSNSWEILYSELSIYESEYSPEDLHN
FIPKIRGLMKSESVEIIQTTSYKLKSELCIYSPFENLDFHFFIRDILRSK
SDANNFNAD*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR040044SRR1L
IPR012942SRR1-like
Vocabulary: molecular function
TermDefinition
GO:0003824catalytic activity
GO:0016740transferase activity
GO:0016746transferase activity, transferring acyl groups
GO:0016747transferase activity, transferring acyl groups other than amino-acyl groups
Vocabulary: biological process
TermDefinition
GO:0008152metabolic process
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR012942SRR1-like domainPFAMPF07985SRR1coord: 73..125
e-value: 1.2E-14
score: 54.0
IPR040044SRR1-like proteinPANTHERPTHR28626FAMILY NOT NAMEDcoord: 16..242