Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine/arginine-rich splicing factor 1.

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_1 g11381 g11381.t2 TSS g11381.t2 15846776 15846776
chr_1 g11381 g11381.t2 isoform g11381.t2 15846807 15847773
chr_1 g11381 g11381.t2 exon g11381.t2.exon1 15846807 15846942
chr_1 g11381 g11381.t2 cds g11381.t2.CDS1 15846807 15846942
chr_1 g11381 g11381.t2 exon g11381.t2.exon2 15847020 15847104
chr_1 g11381 g11381.t2 cds g11381.t2.CDS2 15847020 15847104
chr_1 g11381 g11381.t2 exon g11381.t2.exon3 15847175 15847773
chr_1 g11381 g11381.t2 cds g11381.t2.CDS3 15847175 15847580
chr_1 g11381 g11381.t2 TTS g11381.t2 15848129 15848129

Sequences

>g11381.t2 Gene=g11381 Length=820
ATGGCTCACAGAAGTAGTGATTCAAATAACAGAATTTATGTAGGAAATTTACCACCGGAT
ATTAGATCAAAAGATGTAGAGGATCTCTTCTTTCGTTTTGGAAAGGTTTCTTTCGTAGAT
TTAAAGAATCGAAGAGGTCCACCTTTTGCATTTGTCGAATTTGAGGATCATCGTGATGCA
TCGGATGCAGTCAAAGCACGTAATAACTACGATTATGATGGATATAAATTGAGAGTTGAA
TTTCCAAGAGGAGGTGGGCCAGGATCATACAGAGGTGGTGGAAGATCCAATAACGATCGT
GGAAGTGGAAGGAGTGGTGGTAACAATAATAGACCAGCCGCAAGACGAAGTCAATATCGT
GTTATGGTCACTGGTTTGCCTTCGAGTGGTTCATGGCAAGATTTAAAAGATCATATGAGA
GAAGCAGGTGATGTGTGCTTTGCCGATGTTTATAAAGATGGGTCAGGTGTGGTCGAGTTT
CTACGACACGAAGATATGAAATACGCTATAAAGAAATTGGACGATTCGCGATTTCGATCA
CATGAAGGCGAGGTAGCTTACATACGTATAAAAGAAGATAGTGGCTCATCTCATGATACT
CGCAGAGACTATAGAGATGATGGGTAAATAATAATTTAATTTCTATCCCATTTTATCTAT
TTAAAATCTGTATTCTCTTTGTATTTACAGTAGCTATGGCCGTTCGCGTTCTCGTTCTCG
CTCGCCATATTCGCCACGAAAACGTCGGGGTTCTCCTGTTTATAATGAATTCAGACCACG
CGCTTCTCGCAGTCGTTCACGATCTTATAATAACTATTAA

>g11381.t2 Gene=g11381 Length=208
MAHRSSDSNNRIYVGNLPPDIRSKDVEDLFFRFGKVSFVDLKNRRGPPFAFVEFEDHRDA
SDAVKARNNYDYDGYKLRVEFPRGGGPGSYRGGGRSNNDRGSGRSGGNNNRPAARRSQYR
VMVTGLPSSGSWQDLKDHMREAGDVCFADVYKDGSGVVEFLRHEDMKYAIKKLDDSRFRS
HEGEVAYIRIKEDSGSSHDTRRDYRDDG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11381.t2 CDD cd12601 RRM2_SRSF1_like 119 192 1.15784E-49
7 g11381.t2 Gene3D G3DSA:3.30.70.330 - 1 89 1.9E-24
6 g11381.t2 Gene3D G3DSA:3.30.70.330 - 118 194 9.3E-26
11 g11381.t2 MobiDBLite mobidb-lite consensus disorder prediction 83 118 -
12 g11381.t2 MobiDBLite mobidb-lite consensus disorder prediction 95 115 -
3 g11381.t2 PANTHER PTHR23147:SF44 SERINE/ARGININE-RICH SPLICING FACTOR 1 7 192 1.2E-75
4 g11381.t2 PANTHER PTHR23147 SERINE/ARGININE RICH SPLICING FACTOR 7 192 1.2E-75
1 g11381.t2 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 12 78 1.3E-16
2 g11381.t2 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 121 182 5.0E-11
14 g11381.t2 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 10 84 16.961
13 g11381.t2 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 119 193 10.787
10 g11381.t2 SMART SM00360 rrm1_1 11 80 5.2E-20
9 g11381.t2 SMART SM00360 rrm1_1 120 186 9.0E-8
5 g11381.t2 SUPERFAMILY SSF54928 RNA-binding domain, RBD 8 191 1.22E-35

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: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