General information for g6767.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative THO complex subunit 4.
Parent gene
- The parent gene g6767 is located on chr_2: 18541523..18543877 (+ strand)
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.t11 | TSS | g6767.t11 | 18539688 | 18539688 |
| chr_2 | g6767 | g6767.t11 | isoform | g6767.t11 | 18539830 | 18541940 |
| chr_2 | g6767 | g6767.t11 | exon | g6767.t11.exon1 | 18539830 | 18540015 |
| chr_2 | g6767 | g6767.t11 | cds | g6767.t11.CDS1 | 18539830 | 18540015 |
| chr_2 | g6767 | g6767.t11 | exon | g6767.t11.exon2 | 18540886 | 18541114 |
| chr_2 | g6767 | g6767.t11 | cds | g6767.t11.CDS2 | 18540886 | 18541114 |
| chr_2 | g6767 | g6767.t11 | exon | g6767.t11.exon3 | 18541186 | 18541382 |
| chr_2 | g6767 | g6767.t11 | cds | g6767.t11.CDS3 | 18541186 | 18541382 |
| chr_2 | g6767 | g6767.t11 | exon | g6767.t11.exon4 | 18541444 | 18541940 |
| chr_2 | g6767 | g6767.t11 | cds | g6767.t11.CDS4 | 18541444 | 18541536 |
| chr_2 | g6767 | g6767.t11 | TTS | g6767.t11 | 18541941 | 18541941 |
Sequences
>g6767.t11 Gene=g6767 Length=1109
ATGGATAAGATTGAGATGAGTTTAGATGACATCATAAAACAAAACAAAAAGACATCGGGA
AAAAATCGTCGACCAGGCCTTAGTAATAAGAAAACTACTTCTCCGAATAAGACAAAGAAA
TTTGGAAATGGCGGAATTTTGAAAGGCCGTGGTCGTGGTGGAATCGCACGCTCAAAGTAT
ACTCGGGGTGATGTTAACAGCGCATGGAAACACGATATGTATGAAGGTGGACGAAAATTG
GGAGGAGCATTGGCATTATCAACAGGCGGTAATCGTGGAGTAGGAGGAACCACAAAACTC
GTAGTGTCAAATCTGGATTTCAGCGTTTCTGACTCGGATATTAATGAATTGTTCCAAGAA
TTTGGACCTTTAAAAGCTGCATCCGTTCACTATGACCGTTCCGGCAGATCTCTTGGAACA
GCAGATGTTATTTTTGAACGCCGTAACGACGCTTTAAAGGCTATGAAAACATACAATGGC
GTGCCTCTTGATGGACGGCCTATGAACATATTGATGGCTACTTCAGAAATTGCATCAGCA
AGAGTGCAAAGAGTACCAAGTTTTTCAACTAATAAAGGAGGAGCTCGTTCACCACGCAAA
CCAATAGGTAAAGAGCTGGAAGAAAACCATTCAAACGAAATTTTGCGGGAGGAGCACAAA
AGCGTGGTGGTGGAAAAAAACCAGAAGTCACCATTGATCAATTAAATGCTGAACTTGATG
CGTATACAATGCAATCATAAATAGTATCAGTTTTTGACCCTACACTGTGAATTAGAATTA
TATATATATCAACAGTGTATGAAATGGATAATATTATAAATAATAAGAATTATAAAAAAA
AATTGTGACATTTAATTTTGAAAACAATTCTCTTTATGAGTTAAGAAGTAAGCTGCAACA
ATAACAGCTTTCATTGATTTTAATTTGTAAGCTTTTTCTCATCTTCTCTCAAATTTTTTA
AGTTGAAAAAATAAACCAAAATTCAGAAATACATATGACGATATTAAAAAATTTTCTTTA
ACATCATAACTATAAAACAATACTGATAAATTGTTAAAGAAAGAAGAATTGTGGAATAAA
AATTATAAAAAATATTTTTTTCTGAAAAT
>g6767.t11 Gene=g6767 Length=234
MDKIEMSLDDIIKQNKKTSGKNRRPGLSNKKTTSPNKTKKFGNGGILKGRGRGGIARSKY
TRGDVNSAWKHDMYEGGRKLGGALALSTGGNRGVGGTTKLVVSNLDFSVSDSDINELFQE
FGPLKAASVHYDRSGRSLGTADVIFERRNDALKAMKTYNGVPLDGRPMNILMATSEIASA
RVQRVPSFSTNKGGARSPRKPIGKELEENHSNEILREEHKSVVVEKNQKSPLIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g6767.t11 | CDD | cd12680 | RRM_THOC4 | 98 | 172 | 8.14782E-48 |
| 6 | g6767.t11 | Gene3D | G3DSA:3.30.70.330 | - | 86 | 182 | 2.9E-22 |
| 12 | g6767.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 12 | 48 | - |
| 9 | g6767.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 40 | - |
| 11 | g6767.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 187 | 234 | - |
| 10 | g6767.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 225 | - |
| 3 | g6767.t11 | PANTHER | PTHR19965:SF35 | THO COMPLEX SUBUNIT 4 | 5 | 197 | 3.1E-43 |
| 4 | g6767.t11 | PANTHER | PTHR19965 | RNA AND EXPORT FACTOR BINDING PROTEIN | 5 | 197 | 3.1E-43 |
| 1 | g6767.t11 | Pfam | PF07078 | Forty-two-three protein | 1 | 53 | 1.0E-4 |
| 2 | g6767.t11 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 100 | 168 | 3.4E-14 |
| 13 | g6767.t11 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 98 | 175 | 15.937 |
| 8 | g6767.t11 | SMART | SM00360 | rrm1_1 | 99 | 171 | 2.9E-17 |
| 5 | g6767.t11 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 96 | 199 | 4.16E-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 transcript has been annotated with K12881 (THO complex subunit 4)
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