General information for g4614.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as THO complex subunit 3.
Parent gene
- The parent gene g4614 is located on chr_2: 3598499..3599951 (- 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 | g4614 | g4614.t1 | TTS | g4614.t1 | 3597431 | 3597431 |
| chr_2 | g4614 | g4614.t1 | isoform | g4614.t1 | 3597482 | 3598499 |
| chr_2 | g4614 | g4614.t1 | exon | g4614.t1.exon1 | 3597482 | 3598311 |
| chr_2 | g4614 | g4614.t1 | cds | g4614.t1.CDS1 | 3597482 | 3598311 |
| chr_2 | g4614 | g4614.t1 | exon | g4614.t1.exon2 | 3598370 | 3598499 |
| chr_2 | g4614 | g4614.t1 | cds | g4614.t1.CDS2 | 3598370 | 3598499 |
| chr_2 | g4614 | g4614.t1 | TSS | g4614.t1 | 3598568 | 3598568 |
Sequences
>g4614.t1 Gene=g4614 Length=960
ATGGGAAGCAGTAAACAGAGACTTCAAGGACTTCAGGACTACTTTAAAACAAATAATAAG
ATAAAAGAATTCAGACCACATCAACAAAAAGTTCATTCTGTTCGATTTAATTGTGATGGA
AAAAAATTAGCAAGTGGTTCAAATGATAAAACAGTGGTCGTATATTCAGTTGATCGTGAT
AGAATTACAAAAGATAAATCATATCATGGACATACAGGTCCAGTCGATCAATTAATTTGG
CATCACACAAATGCGGATCTACTCGCGACTGCTTCAGGAGATAAAAGTGTTCGAATTTGG
GATACAAAGATTCAAAAAAATGTCACTACAGTAAATACAAAAGGTGAAAATATAAATATC
ACTTGGAGTAGAGATGGAAATACAATTGCAGTTGGTAATAAGGAAGATCTCATCACATTC
ATTGACACAAGAACTAATAAAATAAGAGCTGAGGAGAAATTCAATTTTGAAATCAATGAA
ATAATGTGGAACAGAACAAGTGATCAAATGTTTTTGACCAGCGGGCAAGGCAGCATTCAC
GTTTTAAGTTATCCAAATCTTGAAGTGCTCAATGTTCTCAAAGCTCATCCAGCAACGAAT
ATTTGTATTGATTTTGATCCATCTGGTAAATATTTTGCTGTTGGCTCAGCAGATGCACTA
ACATCTATTTGGGATGCTGATGAATTGGCCTGCATACGTGTTTTCTCTCGACTTGATTGG
CCAGTAAGAACAGTCAGCTTCAGTCATGACAGCAAACTTATTGCTTCGGCATCAGAAGAT
CATTTTATCGATATTTCATGCATTGAAACAGGTGAAAAAGTTTATGAGATTAAATTAGAT
GCAGCAACATTCTCAATAGCATTTCATCCTAAACAATATTTAATTGCTTTTGCATGTGAT
GATAAGAAAGAAGATGGACGTGATGCAGGTAATTTTAAAGTTTTTGGATTTTCTGAATAA
>g4614.t1 Gene=g4614 Length=319
MGSSKQRLQGLQDYFKTNNKIKEFRPHQQKVHSVRFNCDGKKLASGSNDKTVVVYSVDRD
RITKDKSYHGHTGPVDQLIWHHTNADLLATASGDKSVRIWDTKIQKNVTTVNTKGENINI
TWSRDGNTIAVGNKEDLITFIDTRTNKIRAEEKFNFEINEIMWNRTSDQMFLTSGQGSIH
VLSYPNLEVLNVLKAHPATNICIDFDPSGKYFAVGSADALTSIWDADELACIRVFSRLDW
PVRTVSFSHDSKLIASASEDHFIDISCIETGEKVYEIKLDAATFSIAFHPKQYLIAFACD
DKKEDGRDAGNFKVFGFSE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4614.t1 | Gene3D | G3DSA:2.130.10.10 | - | 11 | 185 | 7.1E-32 |
| 10 | g4614.t1 | Gene3D | G3DSA:2.130.10.10 | - | 186 | 304 | 9.4E-22 |
| 4 | g4614.t1 | PANTHER | PTHR22839 | THO COMPLEX SUBUNIT 3 THO3 | 10 | 317 | 1.8E-116 |
| 6 | g4614.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 43 | 57 | 3.3E-5 |
| 5 | g4614.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 88 | 102 | 3.3E-5 |
| 7 | g4614.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 212 | 226 | 3.3E-5 |
| 1 | g4614.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 19 | 55 | 3.0E-4 |
| 3 | g4614.t1 | Pfam | PF12894 | Anaphase-promoting complex subunit 4 WD40 domain | 84 | 164 | 2.9E-5 |
| 2 | g4614.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 190 | 225 | 8.0E-4 |
| 11 | g4614.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 88 | 102 | - |
| 18 | g4614.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 24 | 276 | 25.496 |
| 20 | g4614.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 24 | 65 | 11.511 |
| 21 | g4614.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 68 | 110 | 13.316 |
| 19 | g4614.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 193 | 234 | 11.377 |
| 17 | g4614.t1 | SMART | SM00320 | WD40_4 | 17 | 56 | 8.4E-8 |
| 16 | g4614.t1 | SMART | SM00320 | WD40_4 | 61 | 101 | 7.4E-8 |
| 14 | g4614.t1 | SMART | SM00320 | WD40_4 | 104 | 142 | 350.0 |
| 13 | g4614.t1 | SMART | SM00320 | WD40_4 | 186 | 225 | 6.9E-5 |
| 12 | g4614.t1 | SMART | SM00320 | WD40_4 | 228 | 267 | 0.92 |
| 15 | g4614.t1 | SMART | SM00320 | WD40_4 | 270 | 316 | 160.0 |
| 8 | g4614.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 17 | 302 | 3.71E-56 |
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:0006406 | mRNA export from nucleus | BP |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12880 (THO complex subunit 3)
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.
