Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative RNA-binding protein squid.

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_3 g1159 g1159.t7 TSS g1159.t7 8422719 8422719
chr_3 g1159 g1159.t7 isoform g1159.t7 8422830 8426879
chr_3 g1159 g1159.t7 exon g1159.t7.exon1 8422830 8422957
chr_3 g1159 g1159.t7 cds g1159.t7.CDS1 8422830 8422957
chr_3 g1159 g1159.t7 exon g1159.t7.exon2 8426427 8426467
chr_3 g1159 g1159.t7 cds g1159.t7.CDS2 8426427 8426467
chr_3 g1159 g1159.t7 exon g1159.t7.exon3 8426535 8426809
chr_3 g1159 g1159.t7 cds g1159.t7.CDS3 8426535 8426809
chr_3 g1159 g1159.t7 exon g1159.t7.exon4 8426874 8426879
chr_3 g1159 g1159.t7 cds g1159.t7.CDS4 8426874 8426879
chr_3 g1159 g1159.t7 TTS g1159.t7 8427624 8427624

Sequences

>g1159.t7 Gene=g1159 Length=450
ATGGCTGATGTACAAGAATACGATAACGGCGAACAAATGCAAGAAGATTTCCAGGGACAA
GGTGATCAATCTGGAGATAGTAACTATCAAAACGGAAATGGAGAAACTCAAGCTCGCGAT
GACGATCGAAAGCTGTTTGTCGGTGGTTTAAGTTGGGAAACAACAGAAAAGGAATTGCGT
GATCATTTTGGACAATATGGTGAAATTGACAGCATCAATGTTAAAACAGATCCTACAACT
GGTCGCTCACGTGGATTTGCATTCATTGTTTATAAAGCAGCTGATTCAATTGATAAAGTT
GTCGCTGCTGGTGATCATATCATTAACAACAAGAAAGTTGATCCTAAAAAAGCCAAGGCA
AGAACTGGCAAAATCTTTGTCGGTGGACTCATTCCAGAAATTAGTGATGATGAAATCAAG
GCATATTTCTCACAATTTGGAAATATTACT

>g1159.t7 Gene=g1159 Length=150
MADVQEYDNGEQMQEDFQGQGDQSGDSNYQNGNGETQARDDDRKLFVGGLSWETTEKELR
DHFGQYGEIDSINVKTDPTTGRSRGFAFIVYKAADSIDKVVAAGDHIINNKKVDPKKAKA
RTGKIFVGGLIPEISDDEIKAYFSQFGNIT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1159.t7 CDD cd12325 RRM1_hnRNPA_hnRNPD_like 45 116 7.50422E-38
5 g1159.t7 Gene3D G3DSA:3.30.70.330 - 2 120 2.6E-27
6 g1159.t7 Gene3D G3DSA:3.30.70.330 - 121 150 2.7E-6
9 g1159.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 44 -
10 g1159.t7 MobiDBLite mobidb-lite consensus disorder prediction 11 35 -
2 g1159.t7 PANTHER PTHR48033:SF8 RNA-BINDING PROTEIN SQUID 9 149 6.4E-62
3 g1159.t7 PANTHER PTHR48033 RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN 9 149 6.4E-62
1 g1159.t7 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 45 112 8.0E-18
12 g1159.t7 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 43 125 17.097
11 g1159.t7 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 123 150 8.586
8 g1159.t7 SMART SM00360 rrm1_1 44 116 8.1E-24
4 g1159.t7 SUPERFAMILY SSF54928 RNA-binding domain, RBD 40 149 3.09E-33

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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