Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Serine/arginine-rich splicing factor 7.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g6631 g6631.t6 isoform g6631.t6 17873965 17876635
chr_2 g6631 g6631.t6 exon g6631.t6.exon1 17873965 17874102
chr_2 g6631 g6631.t6 TTS g6631.t6 17873978 17873978
chr_2 g6631 g6631.t6 exon g6631.t6.exon2 17874162 17874295
chr_2 g6631 g6631.t6 cds g6631.t6.CDS1 17874177 17874295
chr_2 g6631 g6631.t6 exon g6631.t6.exon3 17874357 17874502
chr_2 g6631 g6631.t6 cds g6631.t6.CDS2 17874357 17874502
chr_2 g6631 g6631.t6 exon g6631.t6.exon4 17875894 17875953
chr_2 g6631 g6631.t6 cds g6631.t6.CDS3 17875894 17875953
chr_2 g6631 g6631.t6 exon g6631.t6.exon5 17876009 17876173
chr_2 g6631 g6631.t6 cds g6631.t6.CDS4 17876009 17876173
chr_2 g6631 g6631.t6 exon g6631.t6.exon6 17876230 17876408
chr_2 g6631 g6631.t6 cds g6631.t6.CDS5 17876230 17876408
chr_2 g6631 g6631.t6 exon g6631.t6.exon7 17876633 17876635
chr_2 g6631 g6631.t6 cds g6631.t6.CDS6 17876633 17876635
chr_2 g6631 g6631.t6 TSS g6631.t6 17876690 17876690

Sequences

>g6631.t6 Gene=g6631 Length=825
ATGTCAAAGTCAAATAAAATGTCTCGATACCCTCACGATGCCAAAGTTTATGTTGGCGAT
TTGGGATCGAATGCAGATAAGCAGGAAATTGAAGATGCATTTAGCTACTATGGACCATTA
AGATCAGTTTGGGTAGCGAGAAACCCCCCAGGATTCGCTTTCGTAGAATTTGAAGATGCT
CGTGATGCCGAAGATTCAGTTAGAGGATTAGATGGTCGAACAATTTGTGGACGCCGAGCA
AGAGTTGAATTGTCAACTGGCAAATCAGCACGCGGATTTCGTTCTAGAGGTGGCCGTGGG
CGTTCACCTAATCGTCGAGAAGATCGCTGTTACGAATGTGGAAATAGAGGTCATTTTGCT
CGTGATTGTCGTCGGCGTAATGGAGGAGGAAGTCGTCGTGGTGGCAGATCTCGAAGCCGC
TCTCGATCGCGTAGATCTCGTAGTCACTCGAGAGATCATAGATACAGTCGTTCACCAGCA
GATCGAACAAGAGATCGCAGATCTCATTCAAGCGACCGTAGATCTGCTTCTGAACTTAGC
GAAACACGAAAAAAAAAACATAGTGACAAGTCATGGAAGAGTTCAAGGACAAATTCACCA
CAGTCAGATAGATCTCGAAGAAGTCGTTCCCAAGACACTCAAGCCTCCAATTCGGAACCG
CGTAAAGAGTGAAATGAGATTCATTCCGTTGGTAGTTACATCTTTAAGAACATCTAATAA
TTGCCGTATGACTTACGAGAAAAGTGACCTATTCATCAGTCATACATTATATAATATAAA
TTATAGTTTGAATAAATTGATTTATATTATATAAAAAAAAAATAT

>g6631.t6 Gene=g6631 Length=223
MSKSNKMSRYPHDAKVYVGDLGSNADKQEIEDAFSYYGPLRSVWVARNPPGFAFVEFEDA
RDAEDSVRGLDGRTICGRRARVELSTGKSARGFRSRGGRGRSPNRREDRCYECGNRGHFA
RDCRRRNGGGSRRGGRSRSRSRSRRSRSHSRDHRYSRSPADRTRDRRSHSSDRRSASELS
ETRKKKHSDKSWKSSRTNSPQSDRSRRSRSQDTQASNSEPRKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6631.t6 CDD cd12373 RRM_SRSF3_like 15 87 1.45428E-43
7 g6631.t6 Gene3D G3DSA:3.30.70.330 - 7 88 1.3E-22
6 g6631.t6 Gene3D G3DSA:4.10.60.10 - 89 137 9.6E-8
12 g6631.t6 MobiDBLite mobidb-lite consensus disorder prediction 87 107 -
11 g6631.t6 MobiDBLite mobidb-lite consensus disorder prediction 124 223 -
14 g6631.t6 MobiDBLite mobidb-lite consensus disorder prediction 130 152 -
15 g6631.t6 MobiDBLite mobidb-lite consensus disorder prediction 153 188 -
13 g6631.t6 MobiDBLite mobidb-lite consensus disorder prediction 200 223 -
3 g6631.t6 PANTHER PTHR23147:SF52 SERINE AND ARGININE-RICH-SPLICING FACTOR 7A 3 213 3.7E-46
4 g6631.t6 PANTHER PTHR23147 SERINE/ARGININE RICH SPLICING FACTOR 3 213 3.7E-46
2 g6631.t6 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 16 79 1.0E-16
1 g6631.t6 Pfam PF00098 Zinc knuckle 109 124 1.8E-5
17 g6631.t6 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 14 87 17.063
16 g6631.t6 ProSiteProfiles PS50158 Zinc finger CCHC-type profile. 109 125 10.79
10 g6631.t6 SMART SM00360 rrm1_1 15 83 3.6E-20
9 g6631.t6 SMART SM00343 c2hcfinal6 109 125 0.0017
5 g6631.t6 SUPERFAMILY SSF54928 RNA-binding domain, RBD 11 115 8.69E-26

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0008270 zinc ion binding MF
GO:0003676 nucleic acid binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed