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.t42 TTS g6631.t42 17874363 17874363
chr_2 g6631 g6631.t42 isoform g6631.t42 17874963 17876635
chr_2 g6631 g6631.t42 exon g6631.t42.exon1 17874963 17875337
chr_2 g6631 g6631.t42 cds g6631.t42.CDS1 17875307 17875337
chr_2 g6631 g6631.t42 exon g6631.t42.exon2 17875894 17875953
chr_2 g6631 g6631.t42 cds g6631.t42.CDS2 17875894 17875953
chr_2 g6631 g6631.t42 exon g6631.t42.exon3 17876009 17876173
chr_2 g6631 g6631.t42 cds g6631.t42.CDS3 17876009 17876173
chr_2 g6631 g6631.t42 exon g6631.t42.exon4 17876230 17876402
chr_2 g6631 g6631.t42 cds g6631.t42.CDS4 17876230 17876402
chr_2 g6631 g6631.t42 exon g6631.t42.exon5 17876633 17876635
chr_2 g6631 g6631.t42 cds g6631.t42.CDS5 17876633 17876635
chr_2 g6631 g6631.t42 TSS g6631.t42 17876690 17876690

Sequences

>g6631.t42 Gene=g6631 Length=776
ATGTCAAATAAAATGTCTCGATACCCTCACGATGCCAAAGTTTATGTTGGCGATTTGGGA
TCGAATGCAGATAAGCAGGAAATTGAAGATGCATTTAGCTACTATGGACCATTAAGATCA
GTTTGGGTAGCGAGAAACCCCCCAGGATTCGCTTTCGTAGAATTTGAAGATGCTCGTGAT
GCCGAAGATTCAGTTAGAGGATTAGATGGTCGAACAATTTGTGGACGCCGAGCAAGAGTT
GAATTGTCAACTGGCAAATCAGCACGCGGATTTCGTTCTAGAGGTGGCCGTGGGCGTTCA
CCTAATCGTCGAGAAGATCGCTGTTACGAATGTGGAAATAGAGGTCATTTTGCTCGTGAT
TGTCGTCGGCGTAATGGAGGAGGAAGTCGTCGTGGTGGCAGTCCCTATATCATTATCAAC
AACAAAAAATGAAATCAGTTAACATATAAGTACAAGACATTACGACACATGAAACTAATT
TAATCATCGTGCGTAATCATCTTAAACGTGTGGTACATTGAGCTGGGGTTTTAAAAGCAA
GTGCACAAATTCTGTCGTAAAAGAATTATCTGAATCGAACATTGATCACCTTTCTAAGAA
AGCAATCGGCACAACTTGTAAAATTACGAGTCAACTCGAAAGTATGAGTAAAGATGAAGA
ATTTTTGTTCCTACTTCTTCTTATCCCCTTGGCTTCATGAACGTGTCTCTTCTCGTGTGT
GATATCAAGTTGAGAAACGGTAAACATGTTTCATCGCAGTGCTTTTCTTCCATCAC

>g6631.t42 Gene=g6631 Length=143
MSNKMSRYPHDAKVYVGDLGSNADKQEIEDAFSYYGPLRSVWVARNPPGFAFVEFEDARD
AEDSVRGLDGRTICGRRARVELSTGKSARGFRSRGGRGRSPNRREDRCYECGNRGHFARD
CRRRNGGGSRRGGSPYIIINNKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6631.t42 CDD cd12373 RRM_SRSF3_like 13 85 5.87415E-44
7 g6631.t42 Gene3D G3DSA:3.30.70.330 - 5 85 4.7E-23
6 g6631.t42 Gene3D G3DSA:4.10.60.10 - 86 134 5.3E-9
12 g6631.t42 MobiDBLite mobidb-lite consensus disorder prediction 85 106 -
11 g6631.t42 MobiDBLite mobidb-lite consensus disorder prediction 122 143 -
3 g6631.t42 PANTHER PTHR23147:SF52 SERINE AND ARGININE-RICH-SPLICING FACTOR 7A 4 124 2.3E-44
4 g6631.t42 PANTHER PTHR23147 SERINE/ARGININE RICH SPLICING FACTOR 4 124 2.3E-44
2 g6631.t42 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 14 77 3.9E-17
1 g6631.t42 Pfam PF00098 Zinc knuckle 107 122 9.6E-6
14 g6631.t42 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 12 85 17.063
13 g6631.t42 ProSiteProfiles PS50158 Zinc finger CCHC-type profile. 107 123 10.79
10 g6631.t42 SMART SM00360 rrm1_1 13 81 3.6E-20
9 g6631.t42 SMART SM00343 c2hcfinal6 107 123 0.0017
5 g6631.t42 SUPERFAMILY SSF54928 RNA-binding domain, RBD 9 113 2.71E-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.

Raw TPM values