General information for g12900.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transportin-3.
Parent gene
- The parent gene g12900 is located on chr_1: 26788189..26789033 (- 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 | g12900 | g12900.t4 | isoform | g12900.t4 | 26788189 | 26789033 |
| chr_1 | g12900 | g12900.t4 | exon | g12900.t4.exon1 | 26788189 | 26788856 |
| chr_1 | g12900 | g12900.t4 | cds | g12900.t4.CDS1 | 26788191 | 26788856 |
| chr_1 | g12900 | g12900.t4 | exon | g12900.t4.exon2 | 26788917 | 26789033 |
| chr_1 | g12900 | g12900.t4 | cds | g12900.t4.CDS2 | 26788917 | 26789033 |
| chr_1 | g12900 | g12900.t4 | TSS | g12900.t4 | 26789187 | 26789187 |
| chr_1 | g12900 | g12900.t4 | TTS | g12900.t4 | NA | NA |
Sequences
>g12900.t4 Gene=g12900 Length=785
ATGGAAGAGGAACCTAAAATTGAAGACGTTTTAAATAAAATTTACGATTTATACTGTAAT
CCTGACATTTCTAAAAAAGATCCTGCATCAAAGTATCTTGCAAGCCTACAAGATTCGATT
TATTCATGGAAAATCTCGGATCAATTATTACAGCAAAAGAATGATATGCATTCATGCTAT
TATGCCGCACAGACACTTCGAAGTAAGATACAACACTCATTTCATGAGCTACATGAGTCT
GACTACATTTCTCTACGTGATTCAATTATTGCTCATATAGAGCATATTACGCCAGATACA
AATCCAACGATAGCAAAACAATTATGTTTAGCATTAGCAGATCTATTGCTTTTGATGGCA
TCTTGGATGAAGCCAGTAGATGATTTAATTAAGAAATTCTCACAGAAAACTGATTCCATC
CAACCGCTATTGATGTTGCTAACATTTATACCAGAAGAACTTGATGCTCGATATTTAAGA
ATTGGTGAAAATCGAAGAAAACAAATTCTTAATGAACTCGACACTAGTTCACCTATAATA
CTCAGTTTTCTTCAATCATGCTTGATGATTAACGATACATCTATCCTTCAACATATTTAT
GTCGATGTAATTCAATGCTTTACGGCATGGGTTAAAATGGATTGCATAAATCTAACTGAT
GCGGCTGTTTCTCCAGTGTTTTCTTATGCTTTTAAAATTCTTACTAGTCCTCCTTCAACG
ACCGATGAAAAACAATTGGAAGTTGCTTCTGACTGTGTTTGTGCTATTTTAGAGGCAATT
GTACT
>g12900.t4 Gene=g12900 Length=261
MEEEPKIEDVLNKIYDLYCNPDISKKDPASKYLASLQDSIYSWKISDQLLQQKNDMHSCY
YAAQTLRSKIQHSFHELHESDYISLRDSIIAHIEHITPDTNPTIAKQLCLALADLLLLMA
SWMKPVDDLIKKFSQKTDSIQPLLMLLTFIPEELDARYLRIGENRRKQILNELDTSSPII
LSFLQSCLMINDTSILQHIYVDVIQCFTAWVKMDCINLTDAAVSPVFSYAFKILTSPPST
TDEKQLEVASDCVCAILEAIV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12900.t4 | Gene3D | G3DSA:1.25.10.10 | - | 2 | 261 | 0.0e+00 |
| 3 | g12900.t4 | PANTHER | PTHR12363:SF42 | TRANSPORTIN-3 | 1 | 259 | 0.0e+00 |
| 4 | g12900.t4 | PANTHER | PTHR12363 | TRANSPORTIN 3 AND IMPORTIN 13 | 1 | 259 | 0.0e+00 |
| 1 | g12900.t4 | Pfam | PF03810 | Importin-beta N-terminal domain | 29 | 93 | 3.6e-06 |
| 2 | g12900.t4 | Pfam | PF08389 | Exportin 1-like protein | 103 | 239 | 0.0e+00 |
| 5 | g12900.t4 | SUPERFAMILY | SSF48371 | ARM repeat | 1 | 258 | 0.0e+00 |
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:0031267 | small GTPase binding | MF |
| GO:0006886 | intracellular protein transport | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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