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.t7 TSS g6767.t7 18539688 18539688
chr_2 g6767 g6767.t7 isoform g6767.t7 18539830 18541571
chr_2 g6767 g6767.t7 exon g6767.t7.exon1 18539830 18540005
chr_2 g6767 g6767.t7 cds g6767.t7.CDS1 18539830 18540005
chr_2 g6767 g6767.t7 exon g6767.t7.exon2 18540900 18541114
chr_2 g6767 g6767.t7 cds g6767.t7.CDS2 18540900 18541114
chr_2 g6767 g6767.t7 exon g6767.t7.exon3 18541186 18541377
chr_2 g6767 g6767.t7 cds g6767.t7.CDS3 18541186 18541377
chr_2 g6767 g6767.t7 exon g6767.t7.exon4 18541444 18541571
chr_2 g6767 g6767.t7 cds g6767.t7.CDS4 18541444 18541571
chr_2 g6767 g6767.t7 TTS g6767.t7 18541941 18541941

Sequences

>g6767.t7 Gene=g6767 Length=711
ATGGATAAGATTGAGATGAGTTTAGATGACATCATAAAACAAAACAAAAAGACATCGGGA
AAAAATCGTCGACCAGGCCTTAGTAATAAGAAAACTACTTCTCCGAATAAGACAAAGAAA
TTTGGAAATGGCGGAATTTTGAAAGGCCGTGGTCGTGGTGGAATCGCACGCTCAAACGCA
TGGAAACACGATATGTATGAAGGTGGACGAAAATTGGGAGGAGCATTGGCATTATCAACA
GGCGGTAATCGTGGAGTAGGAGGAACCACAAAACTCGTAGTGTCAAATCTGGATTTCAGC
GTTTCTGACTCGGATATTAATGAATTGTTCCAAGAATTTGGACCTTTAAAAGCTGCATCC
GTTCACTATGACCGTTCCGGCAGATCTCTTGGAACAGCAGATGTTATTTTTGAACGCCGT
AACGACGCTTTAAAGGCTATGAAAACATACAATGGCGTGCCTCTTGATGGACGGCCTATG
AACATATTGATGGCTACTTCAGAAATTGCATCAGCAAGAGTGCAAAGAGTACCAAGTTTT
TCAACTAATAAAGGAGGAGCTCGTTCACCACGCAAACCAATAGGAGCTGGAAGAAAACCA
TTCAAACGAAATTTTGCGGGAGGAGCACAAAAGCGTGGTGGTGGAAAAAAACCAGAAGTC
ACCATTGATCAATTAAATGCTGAACTTGATGCGTATACAATGCAATCATAA

>g6767.t7 Gene=g6767 Length=236
MDKIEMSLDDIIKQNKKTSGKNRRPGLSNKKTTSPNKTKKFGNGGILKGRGRGGIARSNA
WKHDMYEGGRKLGGALALSTGGNRGVGGTTKLVVSNLDFSVSDSDINELFQEFGPLKAAS
VHYDRSGRSLGTADVIFERRNDALKAMKTYNGVPLDGRPMNILMATSEIASARVQRVPSF
STNKGGARSPRKPIGAGRKPFKRNFAGGAQKRGGGKKPEVTIDQLNAELDAYTMQS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6767.t7 CDD cd12680 RRM_THOC4 90 164 7.14316E-48
6 g6767.t7 Gene3D G3DSA:3.30.70.330 - 78 174 2.9E-22
11 g6767.t7 MobiDBLite mobidb-lite consensus disorder prediction 12 48 -
9 g6767.t7 MobiDBLite mobidb-lite consensus disorder prediction 25 40 -
10 g6767.t7 MobiDBLite mobidb-lite consensus disorder prediction 179 222 -
3 g6767.t7 PANTHER PTHR19965:SF35 THO COMPLEX SUBUNIT 4 5 232 2.3E-46
4 g6767.t7 PANTHER PTHR19965 RNA AND EXPORT FACTOR BINDING PROTEIN 5 232 2.3E-46
1 g6767.t7 Pfam PF07078 Forty-two-three protein 1 53 8.4E-5
2 g6767.t7 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 92 160 3.5E-14
12 g6767.t7 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 90 167 15.937
8 g6767.t7 SMART SM00360 rrm1_1 91 163 2.9E-17
5 g6767.t7 SUPERFAMILY SSF54928 RNA-binding domain, RBD 88 193 3.49E-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

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. There were no conditions that were differentially expressed