Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative THO complex subunit 4.

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 g6767 g6767.t20 isoform g6767.t20 18540913 18541940
chr_2 g6767 g6767.t20 exon g6767.t20.exon1 18540913 18541114
chr_2 g6767 g6767.t20 cds g6767.t20.CDS1 18540916 18541114
chr_2 g6767 g6767.t20 exon g6767.t20.exon2 18541186 18541377
chr_2 g6767 g6767.t20 cds g6767.t20.CDS2 18541186 18541377
chr_2 g6767 g6767.t20 exon g6767.t20.exon3 18541451 18541940
chr_2 g6767 g6767.t20 cds g6767.t20.CDS3 18541451 18541536
chr_2 g6767 g6767.t20 TTS g6767.t20 18541941 18541941
chr_2 g6767 g6767.t20 TSS g6767.t20 NA NA

Sequences

>g6767.t20 Gene=g6767 Length=884
GATATGTATGAAGGTGGACGAAAATTGGGAGGAGCATTGGCATTATCAACAGGCGGTAAT
CGTGGAGTAGGAGGAACCACAAAACTCGTAGTGTCAAATCTGGATTTCAGCGTTTCTGAC
TCGGATATTAATGAATTGTTCCAAGAATTTGGACCTTTAAAAGCTGCATCCGTTCACTAT
GACCGTTCCGGCAGATCTCTTGGAACAGCAGATGTTATTTTTGAACGCCGTAACGACGCT
TTAAAGGCTATGAAAACATACAATGGCGTGCCTCTTGATGGACGGCCTATGAACATATTG
ATGGCTACTTCAGAAATTGCATCAGCAAGAGTGCAAAGAGTACCAAGTTTTTCAACTAAT
AAAGGAGGAGCTCGTTCACCACGCAAACCAATAGAAGAAAACCATTCAAACGAAATTTTG
CGGGAGGAGCACAAAAGCGTGGTGGTGGAAAAAAACCAGAAGTCACCATTGATCAATTAA
ATGCTGAACTTGATGCGTATACAATGCAATCATAAATAGTATCAGTTTTTGACCCTACAC
TGTGAATTAGAATTATATATATATCAACAGTGTATGAAATGGATAATATTATAAATAATA
AGAATTATAAAAAAAAATTGTGACATTTAATTTTGAAAACAATTCTCTTTATGAGTTAAG
AAGTAAGCTGCAACAATAACAGCTTTCATTGATTTTAATTTGTAAGCTTTTTCTCATCTT
CTCTCAAATTTTTTAAGTTGAAAAAATAAACCAAAATTCAGAAATACATATGACGATATT
AAAAAATTTTCTTTAACATCATAACTATAAAACAATACTGATAAATTGTTAAAGAAAGAA
GAATTGTGGAATAAAAATTATAAAAAATATTTTTTTCTGAAAAT

>g6767.t20 Gene=g6767 Length=158
MYEGGRKLGGALALSTGGNRGVGGTTKLVVSNLDFSVSDSDINELFQEFGPLKAASVHYD
RSGRSLGTADVIFERRNDALKAMKTYNGVPLDGRPMNILMATSEIASARVQRVPSFSTNK
GGARSPRKPIEENHSNEILREEHKSVVVEKNQKSPLIN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g6767.t20 CDD cd12680 RRM_THOC4 26 100 1.97023E-49
5 g6767.t20 Gene3D G3DSA:3.30.70.330 - 14 110 1.1E-22
8 g6767.t20 MobiDBLite mobidb-lite consensus disorder prediction 114 158 -
9 g6767.t20 MobiDBLite mobidb-lite consensus disorder prediction 125 149 -
2 g6767.t20 PANTHER PTHR19965:SF35 THO COMPLEX SUBUNIT 4 26 125 2.0E-37
3 g6767.t20 PANTHER PTHR19965 RNA AND EXPORT FACTOR BINDING PROTEIN 26 125 2.0E-37
1 g6767.t20 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 28 96 1.5E-14
10 g6767.t20 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 26 103 15.937
7 g6767.t20 SMART SM00360 rrm1_1 27 99 2.9E-17
4 g6767.t20 SUPERFAMILY SSF54928 RNA-binding domain, RBD 24 127 1.75E-23

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