Transcription elongation factor SPT4

Overview
NameTranscription elongation factor SPT4
Smed IDSMED30012706
Length (bp)545
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 Transcription elongation factor SPT4 (SMED30012706) t-SNE clustered cells

Violin plots show distribution of expression levels for Transcription elongation factor SPT4 (SMED30012706) 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 Transcription elongation factor SPT4 (SMED30012706) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Transcription elongation factor SPT4 (SMED30012706) 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



SMED30012706

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
X1 cellSMED30012706 SmedASXL_006820SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30012706 SmedASXL_006820SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
parenchymal cellSMED30012706 dd_Smed_v4_2763_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 Transcription elongation factor SPT4 vs. Ensembl Human
Match: SUPT4H1 (SPT4 homolog, DSIF elongation factor subunit [Source:HGNC Symbol;Acc:HGNC:11467])

HSP 1 Score: 153.295 bits (386), Expect = 5.912e-48
Identity = 68/112 (60.71%), Postives = 90/112 (80.36%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+ +IAMM P+ SWV+KWQ +     G+YA SVTG+LP  +V++LK +GV Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Human
Match: SUPT4H1 (SPT4 homolog, DSIF elongation factor subunit [Source:HGNC Symbol;Acc:HGNC:11467])

HSP 1 Score: 153.295 bits (386), Expect = 5.912e-48
Identity = 68/112 (60.71%), Postives = 90/112 (80.36%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+ +IAMM P+ SWV+KWQ +     G+YA SVTG+LP  +V++LK +GV Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Human
Match: SUPT4H1 (SPT4 homolog, DSIF elongation factor subunit [Source:HGNC Symbol;Acc:HGNC:11467])

HSP 1 Score: 117.472 bits (293), Expect = 6.369e-34
Identity = 51/90 (56.67%), Postives = 69/90 (76.67%), Query Frame = 1 
Query:  124 KTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            +TI+QFEY GCDNC+  + MKGNRE V + TSS+F+ +IAMM P+ SWV+KWQ +     G+YA SVTG+LP  +V++LK +GV Y+SRD
Sbjct:   14 QTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRD 103
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Human
Match: SUPT4H1 (SPT4 homolog, DSIF elongation factor subunit [Source:HGNC Symbol;Acc:HGNC:11467])

HSP 1 Score: 90.8929 bits (224), Expect = 5.301e-24
Identity = 40/71 (56.34%), Postives = 54/71 (76.06%), Query Frame = 1 
Query:  181 MKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            MKGNRE V + TSS+F+ +IAMM P+ SWV+KWQ +     G+YA SVTG+LP  +V++LK +GV Y+SRD
Sbjct:    1 MKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRD 71
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Celegans
Match: spt-4 (Transcription elongation factor SPT4 [Source:UniProtKB/Swiss-Prot;Acc:Q9TZ93])

HSP 1 Score: 120.553 bits (301), Expect = 1.984e-35
Identity = 54/109 (49.54%), Postives = 78/109 (71.56%), Query Frame = 1 
Query:   70 TIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRDR 396
            ++P +LRNLRACLLCS+VK++E F+  GC+NCE V+ +KG+ E V + TS+N++ +IA M  + SWV KWQ + +   GMYA SV+G LP ++V +LK  GV Y+   R
Sbjct:    4 SVPADLRNLRACLLCSLVKSVESFQKEGCENCEDVLHLKGDEEKVYDCTSANYDGMIAAMSNNESWVCKWQKMQRKVKGMYAISVSGVLPNNIVSELKSLGVRYKPNQR 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Fly
Match: spt4 (gene:FBgn0028683 transcript:FBtr0087840)

HSP 1 Score: 141.739 bits (356), Expect = 1.043e-43
Identity = 60/115 (52.17%), Postives = 88/115 (76.52%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRDRSQ 402
            M+ + IPK+LR LRACL+CS+VK+ +QFE  GC+NCE  + MK N++ V + TS+NF+ +IA+  P  SWVAKWQ + +   G+YA SV+G LP S ++D+K++G++Y+SRDRSQ
Sbjct:    1 MAFDAIPKDLRGLRACLVCSLVKSFDQFETDGCENCEEFLRMKNNKDNVYDHTSNNFDGIIALTTPTDSWVAKWQRLSRFTRGIYAISVSGTLPQSTLRDMKNRGIVYKSRDRSQ 115
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Zebrafish
Match: supt4h1 (SPT4 homolog, DSIF elongation factor subunit [Source:NCBI gene;Acc:436782])

HSP 1 Score: 157.918 bits (398), Expect = 5.310e-50
Identity = 73/112 (65.18%), Postives = 90/112 (80.36%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            MS ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNCE  + MKGNRE V E TSS+F+ +IAMM P+ SWVAKWQ I     G+YA +VTG+LP  VV++LK +GV+Y SRD
Sbjct:    1 MSLETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCESYLQMKGNREMVYECTSSSFDGVIAMMSPEDSWVAKWQRIGNFKPGVYAVTVTGRLPPGVVRELKSRGVIYRSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Xenopus
Match: supt4h1 (SPT4 homolog, DSIF elongation factor subunit [Source:NCBI gene;Acc:549433])

HSP 1 Score: 156.762 bits (395), Expect = 2.462e-49
Identity = 70/112 (62.50%), Postives = 91/112 (81.25%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+ ++AMM PD SWV+KWQ I     G+YA SVTG+LP  +V++LK +GVLY+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIVAMMSPDDSWVSKWQRITNFKPGVYAVSVTGRLPQGIVRELKSRGVLYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Mouse
Match: Supt4a (SPT4A, DSIF elongation factor subunit [Source:MGI Symbol;Acc:MGI:107416])

HSP 1 Score: 153.295 bits (386), Expect = 4.059e-48
Identity = 68/112 (60.71%), Postives = 90/112 (80.36%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+ +IAMM P+ SWV+KWQ +     G+YA SVTG+LP  +V++LK +GV Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Mouse
Match: Supt4a (SPT4A, DSIF elongation factor subunit [Source:MGI Symbol;Acc:MGI:107416])

HSP 1 Score: 92.4337 bits (228), Expect = 1.547e-24
Identity = 43/76 (56.58%), Postives = 55/76 (72.37%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQH 285
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+  +A  V   S     Q 
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGCLARAVALGSCCGPLQQ 76
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Mouse
Match: Supt4a (SPT4A, DSIF elongation factor subunit [Source:MGI Symbol;Acc:MGI:107416])

HSP 1 Score: 88.5817 bits (218), Expect = 8.371e-23
Identity = 39/58 (67.24%), Postives = 50/58 (86.21%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFN 231
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFD 58
[Close]
BLAST of Transcription elongation factor SPT4 vs. UniProt/SwissProt
Match: sp|Q6DGQ0|SPT4H_DANRE (Transcription elongation factor SPT4 OS=Danio rerio OX=7955 GN=supt4h1 PE=3 SV=1)

HSP 1 Score: 157.918 bits (398), Expect = 4.009e-49
Identity = 73/112 (65.18%), Postives = 90/112 (80.36%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            MS ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNCE  + MKGNRE V E TSS+F+ +IAMM P+ SWVAKWQ I     G+YA +VTG+LP  VV++LK +GV+Y SRD
Sbjct:    1 MSLETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCESYLQMKGNREMVYECTSSSFDGVIAMMSPEDSWVAKWQRIGNFKPGVYAVTVTGRLPPGVVRELKSRGVIYRSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. UniProt/SwissProt
Match: sp|Q5HZ97|SPT4H_XENLA (Transcription elongation factor SPT4 OS=Xenopus laevis OX=8355 GN=supt4h1 PE=3 SV=1)

HSP 1 Score: 155.606 bits (392), Expect = 3.975e-48
Identity = 69/112 (61.61%), Postives = 91/112 (81.25%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+ ++AMM PD SWV+KWQ I     G+YA SVTG+LP  +V++LK +GV+Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIVAMMSPDDSWVSKWQRITNFKPGVYAVSVTGRLPQGIVRELKSRGVVYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. UniProt/SwissProt
Match: sp|Q4R941|SPT4H_MACFA (Transcription elongation factor SPT4 OS=Macaca fascicularis OX=9541 GN=SUPT4H1 PE=3 SV=1)

HSP 1 Score: 153.295 bits (386), Expect = 2.839e-47
Identity = 68/112 (60.71%), Postives = 90/112 (80.36%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+ +IAMM P+ SWV+KWQ +     G+YA SVTG+LP  +V++LK +GV Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. UniProt/SwissProt
Match: sp|P63272|SPT4H_HUMAN (Transcription elongation factor SPT4 OS=Homo sapiens OX=9606 GN=SUPT4H1 PE=1 SV=1)

HSP 1 Score: 153.295 bits (386), Expect = 2.839e-47
Identity = 68/112 (60.71%), Postives = 90/112 (80.36%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+ +IAMM P+ SWV+KWQ +     G+YA SVTG+LP  +V++LK +GV Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. UniProt/SwissProt
Match: sp|Q3SYX6|SPT4H_BOVIN (Transcription elongation factor SPT4 OS=Bos taurus OX=9913 GN=SUPT4H1 PE=3 SV=1)

HSP 1 Score: 153.295 bits (386), Expect = 2.839e-47
Identity = 68/112 (60.71%), Postives = 90/112 (80.36%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNC+  + MKGNRE V + TSS+F+ +IAMM P+ SWV+KWQ +     G+YA SVTG+LP  +V++LK +GV Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. TrEMBL
Match: A0A3Q1HR72 (Transcription elongation factor SPT4 OS=Anabas testudineus OX=64144 PE=3 SV=1)

HSP 1 Score: 159.844 bits (403), Expect = 2.209e-47
Identity = 74/112 (66.07%), Postives = 91/112 (81.25%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNCE  + MKGNRE V E TSS+F+ +IAMM PD SWVAKWQ I     G+YA SVTG+LP  VV++LK +GV+Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCESYLQMKGNREMVYECTSSSFDGVIAMMSPDDSWVAKWQRIGNFKPGVYAVSVTGRLPPGVVRELKSRGVIYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. TrEMBL
Match: A0A4U5V704 (Transcription elongation factor SPT4 OS=Collichthys lucidus OX=240159 GN=D9C73_017729 PE=3 SV=1)

HSP 1 Score: 159.844 bits (403), Expect = 2.437e-47
Identity = 73/112 (65.18%), Postives = 91/112 (81.25%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNCE  + MKGNRE V E TSS+F+ +IAMM P+ SWVAKWQ I     G+YA SVTG+LP  VV++LK +GV+Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCESYLQMKGNREMVYECTSSSFDGVIAMMSPEDSWVAKWQRIGSFKPGVYAVSVTGRLPAGVVRELKSRGVIYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. TrEMBL
Match: A0A5N5JW97 (Uncharacterized protein OS=Pangasianodon hypophthalmus OX=310915 GN=PHYPO_G00159490 PE=4 SV=1)

HSP 1 Score: 159.073 bits (401), Expect = 4.543e-47
Identity = 73/112 (65.18%), Postives = 91/112 (81.25%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            MS ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNCE  + MKGNRE V E TSS+F+ +IAMM P+ SWVAKWQ I    +G+YA +VTG+LP  VV++LK +GV+Y SRD
Sbjct:    1 MSLETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCESYLQMKGNREMVYECTSSSFDGVIAMMSPEDSWVAKWQRIGNFKAGVYAVTVTGRLPPGVVRELKSRGVIYRSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. TrEMBL
Match: E3TFQ2 (Transcription elongation factor SPT4 OS=Ictalurus punctatus OX=7998 GN=SPT4H PE=2 SV=1)

HSP 1 Score: 159.073 bits (401), Expect = 5.470e-47
Identity = 73/112 (65.18%), Postives = 91/112 (81.25%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            MS ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNCE  + MKGNRE V E TSS+F+ +IAMM P+ SWVAKWQ I    +G+YA +VTG+LP  VV++LK +GV+Y SRD
Sbjct:    1 MSLETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCESCLQMKGNREMVYECTSSSFDGVIAMMSPEDSWVAKWQRIGNFKAGVYAVTVTGRLPPGVVRELKSRGVIYRSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. TrEMBL
Match: A0A1A8F9C6 (Transcription elongation factor SPT4 OS=Nothobranchius korthausae OX=1143690 GN=SUPT4H1 PE=3 SV=1)

HSP 1 Score: 158.688 bits (400), Expect = 6.659e-47
Identity = 73/112 (65.18%), Postives = 91/112 (81.25%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNCE  + MKGNRE V E TSS+F+ +IAMM P+ SWVAKWQ I     G+YA SVTG+LP  VV++LK +GV+Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCESFLQMKGNREMVYECTSSSFDGVIAMMSPEDSWVAKWQRIGNFKPGVYAVSVTGRLPPGVVRELKSRGVIYKSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Cavefish
Match: supt4h1 (SPT4 homolog, DSIF elongation factor subunit [Source:NCBI gene;Acc:103021993])

HSP 1 Score: 158.303 bits (399), Expect = 4.308e-50
Identity = 72/112 (64.29%), Postives = 91/112 (81.25%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            MS ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNCE  + MKGNRE V E TSS+F+ ++AMM P+ SWVAKWQ I    +G+YA +VTG+LP  VV++LK +GV+Y SRD
Sbjct:    1 MSLETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCESYLQMKGNREMVYECTSSSFDGVLAMMSPEDSWVAKWQRIGNFKAGVYAVTVTGRLPPGVVRELKSRGVIYRSRD 112
[Close]
BLAST of Transcription elongation factor SPT4 vs. Ensembl Yeast
Match: SPT4 (Spt4p/5p (DSIF) transcription elongation factor complex subunit; the Spt4/5 complex binds to ssRNA in a sequence-specific manner, and along with RNAP I and II has multiple roles regulating transcriptional elongation, RNA processing, quality control, and transcription-coupled repair; localizes to kinetochores and heterochromatin, influencing chromosomal dynamics and silencing; required for transcription through long trinucleotide repeats in ORFs and non-protein coding regions [Source:SGD;Acc:S000003295])

HSP 1 Score: 87.4261 bits (215), Expect = 1.954e-23
Identity = 45/102 (44.12%), Postives = 59/102 (57.84%), Query Frame = 1 
Query:   97 RACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRDRSQ 402
            RAC+LC +V+T  +F   GC NC+G+    G   +  E TS +F  L+ M  P  SWVAKW  +D   +GMYA  V G+LP  VV+ L H    Y+ RD SQ
Sbjct:    5 RACMLCGIVQTTNEFNRDGCPNCQGIFEEAGV--STMECTSPSFEGLVGMCKPTKSWVAKWLSVDHSIAGMYAIKVDGRLPAEVVELLPH----YKPRDGSQ 100
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Nematostella
Match: EDO41912 (Transcription elongation factor SPT4 [Source:UniProtKB/TrEMBL;Acc:A7S2Z5])

HSP 1 Score: 143.28 bits (360), Expect = 1.132e-44
Identity = 63/114 (55.26%), Postives = 87/114 (76.32%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRDRS 399
            M+ ETIPKELRNLRACLLCS++KT+EQFEY GC+NCE  + +K N+E +   TS NF+ +I+++  + SWVA+WQ I+    G YA SVTG+LP  +V++LK +G+ Y SRDR+
Sbjct:    1 MAMETIPKELRNLRACLLCSLIKTLEQFEYDGCENCEKYLRLKNNKENILSCTSPNFDGVISIISTEDSWVARWQRIESKVKGCYAVSVTGKLPSHIVRELKSRGITYTSRDRT 114
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Medaka
Match: supt4h1 (SPT4 homolog, DSIF elongation factor subunit [Source:NCBI gene;Acc:101165335])

HSP 1 Score: 156.762 bits (395), Expect = 1.791e-49
Identity = 73/112 (65.18%), Postives = 90/112 (80.36%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRD 393
            M+ ET+PK+LR+LRACLLCS+VKTI+QFEY GCDNCE  + MKGNRE V E TSS+F+ +IAMM P+ SWVAKWQ I     G+YA SVTG+LP  VV++LK +GV Y+SRD
Sbjct:    1 MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCEAYLQMKGNREMVYECTSSSFDGVIAMMSPEDSWVAKWQRIGNFKPGVYAVSVTGRLPPGVVRELKSRGVNYKSRD 112
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BLAST of Transcription elongation factor SPT4 vs. Planmine SMEST
Match: SMESG000006978.1 (SMESG000006978.1)

HSP 1 Score: 243.432 bits (620), Expect = 6.231e-84
Identity = 115/115 (100.00%), Postives = 115/115 (100.00%), Query Frame = 1 
Query:   58 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRDRSQ 402
            MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRDRSQ
Sbjct:    1 MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVNELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKDLKHKGVLYESRDRSQ 115
The following BLAST results are available for this feature:
BLAST of Transcription elongation factor SPT4 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 4
Match NameE-valueIdentityDescription
SUPT4H15.912e-4860.71SPT4 homolog, DSIF elongation factor subunit [Sour... [more]
SUPT4H15.912e-4860.71SPT4 homolog, DSIF elongation factor subunit [Sour... [more]
SUPT4H16.369e-3456.67SPT4 homolog, DSIF elongation factor subunit [Sour... [more]
SUPT4H15.301e-2456.34SPT4 homolog, DSIF elongation factor subunit [Sour... [more]
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1
Match NameE-valueIdentityDescription
spt-41.984e-3549.54Transcription elongation factor SPT4 [Source:UniP... [more]
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
spt41.043e-4352.17gene:FBgn0028683 transcript:FBtr0087840[more]
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
supt4h15.310e-5065.18SPT4 homolog, DSIF elongation factor subunit [Sour... [more]
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
supt4h12.462e-4962.50SPT4 homolog, DSIF elongation factor subunit [Sour... [more]
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 3
Match NameE-valueIdentityDescription
Supt4a4.059e-4860.71SPT4A, DSIF elongation factor subunit [Source:MGI ... [more]
Supt4a1.547e-2456.58SPT4A, DSIF elongation factor subunit [Source:MGI ... [more]
Supt4a8.371e-2367.24SPT4A, DSIF elongation factor subunit [Source:MGI ... [more]
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BLAST of Transcription elongation factor SPT4 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 5
Match NameE-valueIdentityDescription
sp|Q6DGQ0|SPT4H_DANRE4.009e-4965.18Transcription elongation factor SPT4 OS=Danio reri... [more]
sp|Q5HZ97|SPT4H_XENLA3.975e-4861.61Transcription elongation factor SPT4 OS=Xenopus la... [more]
sp|Q4R941|SPT4H_MACFA2.839e-4760.71Transcription elongation factor SPT4 OS=Macaca fas... [more]
sp|P63272|SPT4H_HUMAN2.839e-4760.71Transcription elongation factor SPT4 OS=Homo sapie... [more]
sp|Q3SYX6|SPT4H_BOVIN2.839e-4760.71Transcription elongation factor SPT4 OS=Bos taurus... [more]
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BLAST of Transcription elongation factor SPT4 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3Q1HR722.209e-4766.07Transcription elongation factor SPT4 OS=Anabas tes... [more]
A0A4U5V7042.437e-4765.18Transcription elongation factor SPT4 OS=Collichthy... [more]
A0A5N5JW974.543e-4765.18Uncharacterized protein OS=Pangasianodon hypophtha... [more]
E3TFQ25.470e-4765.18Transcription elongation factor SPT4 OS=Ictalurus ... [more]
A0A1A8F9C66.659e-4765.18Transcription elongation factor SPT4 OS=Nothobranc... [more]
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
supt4h14.308e-5064.29SPT4 homolog, DSIF elongation factor subunit [Sour... [more]
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BLAST of Transcription elongation factor SPT4 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 Transcription elongation factor SPT4 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
SPT41.954e-2344.12Spt4p/5p (DSIF) transcription elongation factor co... [more]
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO419121.132e-4455.26Transcription elongation factor SPT4 [Source:UniP... [more]
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BLAST of Transcription elongation factor SPT4 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
supt4h11.791e-4965.18SPT4 homolog, DSIF elongation factor subunit [Sour... [more]
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BLAST of Transcription elongation factor SPT4 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000006978.16.231e-84100.00SMESG000006978.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012706 ID=SMED30012706|Name=Transcription elongation factor SPT4|organism=Schmidtea mediterranea sexual|type=transcript|length=545bp
TTAAATTCTCCGATTATAATTTGATATTTTTAAAATTTTGAATAATCAAA
TAAAAAAATGAGTGATGAAACCATTCCAAAAGAATTAAGAAATCTCCGAG
CTTGTTTATTATGTTCAATGGTCAAAACAATTGAGCAATTCGAGTATTAT
GGATGTGATAATTGTGAAGGCGTAATGCCAATGAAAGGTAATAGAGAGGC
AGTAAACGAACTAACGTCATCAAATTTTAATGACCTTATTGCAATGATGG
TACCAGATTCAAGTTGGGTAGCCAAATGGCAACATATTGATAAACTTTGT
TCCGGTATGTATGCTACAAGTGTTACTGGTCAACTACCTGTATCAGTTGT
CAAAGACTTAAAGCACAAAGGCGTTTTGTATGAAAGTAGAGATAGAAGTC
AATGATTAATGTTTTAAAGTTGTAATATAATGTCTAAATCTTTTATTGTT
TATTTTATAATATTTTGTAATGTACATTTATTCTTGTCTCATACTAGGAT
GAATTGTCTAAATTTCCACATTAATCTGTTTTCAATAAAAATGTG
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protein sequence of SMED30012706-orf-1

>SMED30012706-orf-1 ID=SMED30012706-orf-1|Name=SMED30012706-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=116bp
MSDETIPKELRNLRACLLCSMVKTIEQFEYYGCDNCEGVMPMKGNREAVN
ELTSSNFNDLIAMMVPDSSWVAKWQHIDKLCSGMYATSVTGQLPVSVVKD
LKHKGVLYESRDRSQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR038510Spt4_sf
IPR022800Spt4/RpoE2_Znf
IPR009287Spt4
IPR029040RPABC4/Spt4
Vocabulary: biological process
TermDefinition
GO:0032786positive regulation of DNA-templated transcription, elongation
GO:0006355regulation of transcription, DNA-templated
GO:0006325chromatin organization
GO:0006351transcription, DNA-templated
GO:0006397mRNA processing
GO:0034243regulation of transcription elongation from RNA polymerase II promoter
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0032044DSIF complex
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0000993RNA polymerase II core binding
GO:0003700transcription factor activity, sequence-specific DNA binding
GO:0003727single-stranded RNA binding
GO:0046872metal ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR022800Spt4/RpoE2 zinc fingerSMARTSM01389Spt4_2coord: 13..90
e-value: 1.4E-34
score: 130.9
IPR022800Spt4/RpoE2 zinc fingerPFAMPF06093Spt4coord: 13..90
e-value: 1.1E-27
score: 95.9
IPR022800Spt4/RpoE2 zinc fingerCDDcd07973Spt4coord: 11..108
e-value: 4.27104E-48
score: 147.0
IPR009287Transcription initiation Spt4PIRSFPIRSF025023Spt4coord: 1..115
e-value: 6.0E-45
score: 149.5
IPR009287Transcription initiation Spt4PANTHERPTHR12882SUPPRESSOR OF TY 4coord: 3..113
IPR038510Spt4 superfamilyGENE3DG3DSA:3.30.40.210coord: 1..105
e-value: 2.0E-41
score: 142.1
NoneNo IPR availablePANTHERPTHR12882:SF1TRANSCRIPTION ELONGATION FACTOR SPT4coord: 3..113
IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4SUPERFAMILYSSF63393RNA polymerase subunitscoord: 6..89