General information for g9263.t1
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.t1 | TTS | g9263.t1 | 1362354 | 1362354 |
| chr_1 | g9263 | g9263.t1 | isoform | g9263.t1 | 1362485 | 1365044 |
| chr_1 | g9263 | g9263.t1 | exon | g9263.t1.exon1 | 1362485 | 1362541 |
| chr_1 | g9263 | g9263.t1 | cds | g9263.t1.CDS1 | 1362485 | 1362541 |
| chr_1 | g9263 | g9263.t1 | exon | g9263.t1.exon2 | 1362601 | 1362790 |
| chr_1 | g9263 | g9263.t1 | cds | g9263.t1.CDS2 | 1362601 | 1362790 |
| chr_1 | g9263 | g9263.t1 | exon | g9263.t1.exon3 | 1362853 | 1362940 |
| chr_1 | g9263 | g9263.t1 | cds | g9263.t1.CDS3 | 1362853 | 1362940 |
| chr_1 | g9263 | g9263.t1 | exon | g9263.t1.exon4 | 1362992 | 1363685 |
| chr_1 | g9263 | g9263.t1 | cds | g9263.t1.CDS4 | 1362992 | 1363685 |
| chr_1 | g9263 | g9263.t1 | exon | g9263.t1.exon5 | 1363731 | 1364311 |
| chr_1 | g9263 | g9263.t1 | cds | g9263.t1.CDS5 | 1363731 | 1364311 |
| chr_1 | g9263 | g9263.t1 | exon | g9263.t1.exon6 | 1365032 | 1365044 |
| chr_1 | g9263 | g9263.t1 | cds | g9263.t1.CDS6 | 1365032 | 1365044 |
| chr_1 | g9263 | g9263.t1 | TSS | g9263.t1 | NA | NA |
Sequences
>g9263.t1 Gene=g9263 Length=1623
ATGGCAAGCACTGGTAAAAAAGGCAAAAAGTCCAAAGAAAAGAAATTGTCTCTTCAAGAC
TTTTTAGCAAAATCAAATCCACAAACGGGTAGTGGAACTACTCAAGTTGCTGTTACAAAA
TATAGCAGTTGGGCAGAAGAATGTGAAGAAGATGAGGATCGTAAATTTGAAATTATCCAG
CTACCAACTGCTCCACGCGCTGCTCGAATTTTGGACGATAACTCAATTCCAAATGAAGGT
CCTTTCTATGCACGCGTTTCGAATCTACCCTTCGATATCAATGAAGGAGATGTTGATGAA
TTTTTTCTCGATCAGAACATTCATATACGTGAAATGAGATTGGCGCGTGATGAACAAAAT
GATCGTCTTCGTGGATACGGTCATATTGAGTTTGAAACACGAGATGATCTTTTAGATGCC
ATTATGCTTACTGATCCAATGATTCGCAACAGAAGAATTCGAATTGAGTTCACTGCAGAG
CCCGATAATAGTAGTGGTAGGACTGTTCGTAAACGCTATGACAATTATACACCACGTGAT
TCGGCAAATGAATCAACAAATTGGCGCGATCGAAAAGAATCTAATTTCGAGGCACCACGT
TCAACTTTCCAAAATCGTCATGAATCGAGCAATGATGGTGGCAATGATTCAAATTGGAGA
TTGGGTGAACGACCAAATGATTCACCTCCACCAGAAAGACGTCGTTATGGTAATGATAGA
CGCGATGGTGAAGGTGGAAGGAGAGGACGATATAATGATCGTGAACAACGCGAACAAGTG
CAAGAAGAACGTCCAAAATTAAATCTTGCACCAAGAACTTTGCCACTTCCAGAAATGAAT
TTCCCTAAAGAAGAAGAACTTGAGCGTAATACGAGAAAAATTTCATTAAATGGCGATAGA
GATCATAGTCATGATGATTCAGGTCTTGCAGAAGATGATGAGTCAGAAAGTAAAGAGATA
GCACCAAAACCAAAGCCAGTTCCAGTTCCAAGAGAAAATGTTTTTGGTTCAGCTAAACCA
GTCGATACTACTGCAAGAGAACGTGAAATAGAAGAAAAAATGGAGCAAGAACGTCAAGAA
AAGTTAAAAGCTGAAAAGGAAAAGCGAATGAAGGAGAGAGAAACAACATCACAATCAGAC
ACTAGTAATAAGGATGTCATTGTGATTCGAACGGAAAGTTCACGGCGACAAGATGGCGAA
ACTAATTGGCGAAAACGCGATGAAAATTCATCAAATGGATTTCATGACAATAAAAGTCGT
GGCGGAGGAAATCGTCAAATGGGCAGAAGTTTTCGTTCATTTTCTCATTTTTCAGGTGAC
GATCGTCCACGACAATTTAATAAAGATAATCGCGATAATCGAAACTTTAATAATCGTGGT
GGTGGAATGAATCGCGATCGAAGAGATAGGGATAACAATATGAGAAGAGGCAATGATCAA
GGGATGCGTCGCAATAATGACTATCATAATTCTGGTGGAAATGAAATGCGACGAGAAGAG
CGTGAACGTGAACCAAGGCGTGAAAGAAATTATGAAATGCCGAAATATGTTGAAAATTCA
GGACCTAACTTAAAAACTTCAAACTTATTTGATGGTTTGGATGAAGAAGTTAATGATGAC
TAA
>g9263.t1 Gene=g9263 Length=540
MASTGKKGKKSKEKKLSLQDFLAKSNPQTGSGTTQVAVTKYSSWAEECEEDEDRKFEIIQ
LPTAPRAARILDDNSIPNEGPFYARVSNLPFDINEGDVDEFFLDQNIHIREMRLARDEQN
DRLRGYGHIEFETRDDLLDAIMLTDPMIRNRRIRIEFTAEPDNSSGRTVRKRYDNYTPRD
SANESTNWRDRKESNFEAPRSTFQNRHESSNDGGNDSNWRLGERPNDSPPPERRRYGNDR
RDGEGGRRGRYNDREQREQVQEERPKLNLAPRTLPLPEMNFPKEEELERNTRKISLNGDR
DHSHDDSGLAEDDESESKEIAPKPKPVPVPRENVFGSAKPVDTTAREREIEEKMEQERQE
KLKAEKEKRMKERETTSQSDTSNKDVIVIRTESSRRQDGETNWRKRDENSSNGFHDNKSR
GGGNRQMGRSFRSFSHFSGDDRPRQFNKDNRDNRNFNNRGGGMNRDRRDRDNNMRRGNDQ
GMRRNNDYHNSGGNEMRREEREREPRRERNYEMPKYVENSGPNLKTSNLFDGLDEEVNDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9263.t1 | Coils | Coil | Coil | 347 | 374 | - |
| 5 | g9263.t1 | Gene3D | G3DSA:3.30.70.330 | - | 72 | 167 | 1.4E-13 |
| 19 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 35 | - |
| 17 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 21 | 35 | - |
| 16 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 162 | 540 | - |
| 11 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 165 | 197 | - |
| 14 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 217 | - |
| 9 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 226 | 265 | - |
| 18 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 279 | 321 | - |
| 8 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 342 | 379 | - |
| 10 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 389 | 414 | - |
| 12 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 415 | 433 | - |
| 15 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 435 | 483 | - |
| 13 | g9263.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 490 | 514 | - |
| 2 | g9263.t1 | PANTHER | PTHR23236 | EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4H | 8 | 381 | 3.5E-37 |
| 3 | g9263.t1 | PANTHER | PTHR23236:SF2 | EUKARYOTIC TRANSLATION INITIATION FACTOR 4B | 8 | 381 | 3.5E-37 |
| 1 | g9263.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 86 | 154 | 1.9E-7 |
| 20 | g9263.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 82 | 160 | 12.833 |
| 7 | g9263.t1 | SMART | SM00360 | rrm1_1 | 83 | 156 | 3.5E-11 |
| 4 | g9263.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 75 | 163 | 7.6E-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.
