General information for g9263.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g9263 is located on chr_1: 1362997..1365044 (- 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_1 | g9263 | g9263.t7 | TTS | g9263.t7 | 1362354 | 1362354 |
| chr_1 | g9263 | g9263.t7 | isoform | g9263.t7 | 1362485 | 1365044 |
| chr_1 | g9263 | g9263.t7 | exon | g9263.t7.exon1 | 1362485 | 1362790 |
| chr_1 | g9263 | g9263.t7 | exon | g9263.t7.exon2 | 1362941 | 1364311 |
| chr_1 | g9263 | g9263.t7 | cds | g9263.t7.CDS1 | 1363686 | 1364311 |
| chr_1 | g9263 | g9263.t7 | exon | g9263.t7.exon3 | 1365032 | 1365044 |
| chr_1 | g9263 | g9263.t7 | cds | g9263.t7.CDS2 | 1365032 | 1365044 |
| chr_1 | g9263 | g9263.t7 | TSS | g9263.t7 | NA | NA |
Sequences
>g9263.t7 Gene=g9263 Length=1690
ATGGCAAGCACTGGTAAAAAAGGCAAAAAGTCCAAAGAAAAGAAATTGTCTCTTCAAGAC
TTTTTAGCAAAATCAAATCCACAAACGGGTAGTGGAACTACTCAAGTTGCTGTTACAAAA
TATAGCAGTTGGGCAGAAGAATGTGAAGAAGATGAGGATCGTAAATTTGAAATTATCCAG
CTACCAACTGCTCCACGCGCTGCTCGAATTTTGGACGATAACTCAATTCCAAATGAAGGT
CCTTTCTATGCACGCGTTTCGAATCTACCCTTCGATATCAATGAAGGAGATGTTGATGAA
TTTTTTCTCGATCAGAACATTCATATACGTGAAATGAGATTGGCGCGTGATGAACAAAAT
GATCGTCTTCGTGGATACGGTCATATTGAGTTTGAAACACGAGATGATCTTTTAGATGCC
ATTATGCTTACTGATCCAATGATTCGCAACAGAAGAATTCGAATTGAGTTCACTGCAGAG
CCCGATAATAGTAGTGGTAGGACTGTTCGTAAACGCTATGACAATTATACACCACGTGAT
TCGGCAAATGAATCAACAAATTGGCGCGATCGAAAAGAATCTAATTTCGAGGCAGTGGAT
TCACGCGATAATAGAGAAAATCGTCGACGCAACTATTAGCCACGTTCAACTTTCCAAAAT
CGTCATGAATCGAGCAATGATGGTGGCAATGATTCAAATTGGAGATTGGGTGAACGACCA
AATGATTCACCTCCACCAGAAAGACGTCGTTATGGTAATGATAGACGCGATGGTGAAGGT
GGAAGGAGAGGACGATATAATGATCGTGAACAACGCGAACAAGTGCAAGAAGAACGTCCA
AAATTAAATCTTGCACCAAGAACTTTGCCACTTCCAGAAATGAATTTCCCTAAAGAAGAA
GAACTTGAGCGTAATACGAGAAAAATTTCATTAAATGGCGATAGAGATCATAGTCATGAT
GATTCAGGTCTTGCAGAAGATGATGAGTCAGAAAGTAAAGAGATAGCACCAAAACCAAAG
CCAGTTCCAGTTCCAAGAGAAAATGTTTTTGGTTCAGCTAAACCAGTCGATACTACTGCA
AGAGAACGTGAAATAGAAGAAAAAATGGAGCAAGAACGTCAAGAAAAGTTAAAAGCTGAA
AAGGAAAAGCGAATGAAGGAGAGAGAAACAACATCACAATCAGACACTAGTAATAAGGAT
GTCATTGTGATTCGAACGGAAAGTTCACGGCGACAAGATGGCGAAACTAATTGGCGAAAA
CGCGATGAAAATTCATCAAATGGATTTCATGACAATAAAAGTCGTGGCGGAGGAAATCGT
CAAATGGGCAGAAGTGAGCTATACATTTTTTATTTTTCAAAGAACTATCAACTTACATGT
TAAGTGGTGGTGGAATGAATCGCGATCGAAGAGATAGGGATAACAATATGAGAAGAGGCA
ATGATCAAGGGATGCGTCGCAATAATGACTATCATAATTCTGGTGGAAATGAAATGCGAC
GAGAAGAGCGTGAACGTGAACCAAGGCGTGAAAGAAATTATGAAATGCCGAAATATGTTG
AAAATTCAGGACCTGTAAGTTCCTAATTATTTATGATTTTTTCATAAAATTTAATAATTG
TTTTCAATTTTAGAACTTAAAAACTTCAAACTTATTTGATGGTTTGGATGAAGAAGTTAA
TGATGACTAA
>g9263.t7 Gene=g9263 Length=212
MASTGKKGKKSKEKKLSLQDFLAKSNPQTGSGTTQVAVTKYSSWAEECEEDEDRKFEIIQ
LPTAPRAARILDDNSIPNEGPFYARVSNLPFDINEGDVDEFFLDQNIHIREMRLARDEQN
DRLRGYGHIEFETRDDLLDAIMLTDPMIRNRRIRIEFTAEPDNSSGRTVRKRYDNYTPRD
SANESTNWRDRKESNFEAVDSRDNRENRRRNY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g9263.t7 | Gene3D | G3DSA:3.30.70.330 | - | 72 | 167 | 2.4E-14 |
| 9 | g9263.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 35 | - |
| 7 | g9263.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 21 | 35 | - |
| 8 | g9263.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 163 | 192 | - |
| 6 | g9263.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 165 | 192 | - |
| 2 | g9263.t7 | PANTHER | PTHR23236 | EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4H | 7 | 208 | 2.1E-26 |
| 3 | g9263.t7 | PANTHER | PTHR23236:SF2 | EUKARYOTIC TRANSLATION INITIATION FACTOR 4B | 7 | 208 | 2.1E-26 |
| 1 | g9263.t7 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 86 | 154 | 3.9E-8 |
| 11 | g9263.t7 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 82 | 160 | 12.833 |
| 5 | g9263.t7 | SMART | SM00360 | rrm1_1 | 83 | 156 | 3.5E-11 |
| 4 | g9263.t7 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 75 | 163 | 1.25E-16 |
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:0097010 | eukaryotic translation initiation factor 4F complex assembly | BP |
| GO:0033592 | RNA strand annealing activity | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03258 (translation initiation factor 4B)
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.
