Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g1625 g1625.t8 TTS g1625.t8 12204643 12204643
chr_3 g1625 g1625.t8 isoform g1625.t8 12204684 12208169
chr_3 g1625 g1625.t8 exon g1625.t8.exon1 12204684 12205135
chr_3 g1625 g1625.t8 cds g1625.t8.CDS1 12205015 12205135
chr_3 g1625 g1625.t8 exon g1625.t8.exon2 12207081 12207264
chr_3 g1625 g1625.t8 cds g1625.t8.CDS2 12207081 12207264
chr_3 g1625 g1625.t8 exon g1625.t8.exon3 12207405 12207549
chr_3 g1625 g1625.t8 cds g1625.t8.CDS3 12207405 12207435
chr_3 g1625 g1625.t8 exon g1625.t8.exon4 12207782 12208169
chr_3 g1625 g1625.t8 TSS g1625.t8 NA NA

Sequences

>g1625.t8 Gene=g1625 Length=1169
ATGTGTAAAAATCGATGTCAGTTAGGAAATTAAATAAATTTTTCAAGAAAATTGTCTTTT
TCATTTTGTAAATTTTAAAATTGAATTTTAATTATTTCATTGAATAATTTACTACAGTTT
TAATAAATAAAAAAAAATCTAAATTAATTTTAAATCAATTCTTAATTTCTACATTCAATT
GAAAAGAGCTTTTTATTAAAAATTTAATTATTTTACAAACCTAACTTCAAATATCATTTC
AACCCTGAATCATGCACATTCTTTTCGATATTTAACTTTAAAAATCAACTTAACTTATTA
TATCATAACATAAAATTAAATTTAAGAAAATATTGAGATTAAAAAATTTATTAAATCGTG
CAGTCTTTGATTATAAATTGATATAAAATGCCTCGATATCGCGAATGGGATTTAAAATGT
AAAGTTTATGTCGGTAATTTAGATCAGAGAGCAACAAAGCATCAAATTGAAGATATATTT
AGTAAATATGGCCCATTAAGAAATGTGTGGGTGGCAAGAAATCCACCAGGTTAGCTTTGC
TTTTGTTGAATTCGAGGACAACCGCGATGCAGAAGATGCGGTAAGAAATTTGGACGGAAG
TCGCGCGTGTGGTAGTCGCATTCGTGTGGAAATGTCAAGTGGCAGAACTAGACATAATCG
AGGCAGTGGCGGTTCAAGCGATAGACGTCGCAATGATCGTGGCAGTGGAAGATACAGATC
ACGTTCGAGAGATAGATCAAGAAGTCCACGCCGATCACCACGTCGTTCAAGACGTTCACG
ATCACGCTCAAGAAGTGGCGAAAGAAGCGACCGTTCTGAATCGCGTGATCGTCGTTAAAA
TTATTTAATTATTTTCTTTGTGTCTTTCAAATATTTTTGTTTAATTTTTTTGATCAAACT
TAAATGCATTTTATTAAAAAACACAATTTTTATGTTCTCGTTTGTGAGAAAAATAATTTA
AAAAACAGGACAAAAAAATTATGAATTTGAATGGTAAAAAATTTTATATGACGATAATTG
AGTTACAATGAATTAATTAATAATTATGTTTTTTGAACTCTCTTTTGCTACTTATTTGTC
TTCTTTAAATGAGTTTCATAAACTCACAAATGAAATAATATTTCCTATAGAAATTTTATT
AACAAAACATAAAAATAAAACACTACTAA

>g1625.t8 Gene=g1625 Length=111
MCGWQEIHQVSFAFVEFEDNRDAEDAVRNLDGSRACGSRIRVEMSSGRTRHNRGSGGSSD
RRRNDRGSGRYRSRSRDRSRSPRRSPRRSRRSRSRSRSGERSDRSESRDRR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g1625.t8 Gene3D G3DSA:3.30.70.330 - 7 81 6.4E-11
5 g1625.t8 MobiDBLite mobidb-lite consensus disorder prediction 39 111 -
8 g1625.t8 MobiDBLite mobidb-lite consensus disorder prediction 44 75 -
7 g1625.t8 MobiDBLite mobidb-lite consensus disorder prediction 76 95 -
6 g1625.t8 MobiDBLite mobidb-lite consensus disorder prediction 96 111 -
2 g1625.t8 PANTHER PTHR23147:SF186 RNA-BINDING PROTEIN 1-RELATED 11 101 5.5E-21
3 g1625.t8 PANTHER PTHR23147 SERINE/ARGININE RICH SPLICING FACTOR 11 101 5.5E-21
1 g1625.t8 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 12 40 3.2E-6
10 g1625.t8 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 11 47 8.757
4 g1625.t8 SUPERFAMILY SSF54928 RNA-binding domain, RBD 11 76 3.99E-13

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. There were no conditions that were differentially expressed