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.t8 TSS g6767.t8 18539688 18539688
chr_2 g6767 g6767.t8 isoform g6767.t8 18539830 18541571
chr_2 g6767 g6767.t8 exon g6767.t8.exon1 18539830 18540015
chr_2 g6767 g6767.t8 cds g6767.t8.CDS1 18539830 18540015
chr_2 g6767 g6767.t8 exon g6767.t8.exon2 18540886 18541114
chr_2 g6767 g6767.t8 cds g6767.t8.CDS2 18540886 18541114
chr_2 g6767 g6767.t8 exon g6767.t8.exon3 18541192 18541377
chr_2 g6767 g6767.t8 cds g6767.t8.CDS3 18541192 18541377
chr_2 g6767 g6767.t8 exon g6767.t8.exon4 18541444 18541571
chr_2 g6767 g6767.t8 cds g6767.t8.CDS4 18541444 18541571
chr_2 g6767 g6767.t8 TTS g6767.t8 18541941 18541941

Sequences

>g6767.t8 Gene=g6767 Length=729
ATGGATAAGATTGAGATGAGTTTAGATGACATCATAAAACAAAACAAAAAGACATCGGGA
AAAAATCGTCGACCAGGCCTTAGTAATAAGAAAACTACTTCTCCGAATAAGACAAAGAAA
TTTGGAAATGGCGGAATTTTGAAAGGCCGTGGTCGTGGTGGAATCGCACGCTCAAAGTAT
ACTCGGGGTGATGTTAACAGCGCATGGAAACACGATATGTATGAAGGTGGACGAAAATTG
GGAGGAGCATTGGCATTATCAACAGGCGGTAATCGTGGAGTAGGAGGAACCACAAAACTC
GTAGTGTCAAATCTGGATTTCAGCGTTTCTGACTCGGATATTAATGAATTGTTCCAAGAA
TTTGGACCTTTAAAAGCTGCATCCGTTCACTATGACCGTTCCGGCAGATCTCTTGCAGAT
GTTATTTTTGAACGCCGTAACGACGCTTTAAAGGCTATGAAAACATACAATGGCGTGCCT
CTTGATGGACGGCCTATGAACATATTGATGGCTACTTCAGAAATTGCATCAGCAAGAGTG
CAAAGAGTACCAAGTTTTTCAACTAATAAAGGAGGAGCTCGTTCACCACGCAAACCAATA
GGAGCTGGAAGAAAACCATTCAAACGAAATTTTGCGGGAGGAGCACAAAAGCGTGGTGGT
GGAAAAAAACCAGAAGTCACCATTGATCAATTAAATGCTGAACTTGATGCGTATACAATG
CAATCATAA

>g6767.t8 Gene=g6767 Length=242
MDKIEMSLDDIIKQNKKTSGKNRRPGLSNKKTTSPNKTKKFGNGGILKGRGRGGIARSKY
TRGDVNSAWKHDMYEGGRKLGGALALSTGGNRGVGGTTKLVVSNLDFSVSDSDINELFQE
FGPLKAASVHYDRSGRSLADVIFERRNDALKAMKTYNGVPLDGRPMNILMATSEIASARV
QRVPSFSTNKGGARSPRKPIGAGRKPFKRNFAGGAQKRGGGKKPEVTIDQLNAELDAYTM
QS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6767.t8 CDD cd12680 RRM_THOC4 98 170 8.24727E-44
6 g6767.t8 Gene3D G3DSA:3.30.70.330 - 86 180 5.2E-19
11 g6767.t8 MobiDBLite mobidb-lite consensus disorder prediction 12 48 -
9 g6767.t8 MobiDBLite mobidb-lite consensus disorder prediction 25 40 -
10 g6767.t8 MobiDBLite mobidb-lite consensus disorder prediction 185 228 -
3 g6767.t8 PANTHER PTHR19965:SF35 THO COMPLEX SUBUNIT 4 5 238 4.4E-43
4 g6767.t8 PANTHER PTHR19965 RNA AND EXPORT FACTOR BINDING PROTEIN 5 238 4.4E-43
1 g6767.t8 Pfam PF07078 Forty-two-three protein 1 53 1.1E-4
2 g6767.t8 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 100 166 1.8E-11
12 g6767.t8 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 98 173 14.436
8 g6767.t8 SMART SM00360 rrm1_1 99 169 1.6E-13
5 g6767.t8 SUPERFAMILY SSF54928 RNA-binding domain, RBD 96 199 1.05E-19

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