Gene loci information

Transcript annotation

  • This transcript has been annotated as Transportin-1.

Parent gene

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_3 g3693 g3693.t6 isoform g3693.t6 27482046 27483375
chr_3 g3693 g3693.t6 exon g3693.t6.exon1 27482046 27483021
chr_3 g3693 g3693.t6 cds g3693.t6.CDS1 27482047 27483021
chr_3 g3693 g3693.t6 exon g3693.t6.exon2 27483118 27483256
chr_3 g3693 g3693.t6 cds g3693.t6.CDS2 27483118 27483219
chr_3 g3693 g3693.t6 exon g3693.t6.exon3 27483353 27483375
chr_3 g3693 g3693.t6 TSS g3693.t6 NA NA
chr_3 g3693 g3693.t6 TTS g3693.t6 NA NA

Sequences

>g3693.t6 Gene=g3693 Length=1138
GACATCACATTAGATAAAAGAAGACATTCGCACCATAATATTTTTCCATTTTTACCAAAA
ATGACACATTGGGAGCCACAACCAGAAGGTTTAAATCAAATAATTACACTTCTTAAACAG
AGTCAATCGACAGATAATCAAATTCAAAGAAATGTTCAAATGAAATTAGAAGAATTGAAT
AGATATCCTGATTTTAACAACTATTTAATTTACGTTCTTACGAAGTTGACTACTCAAGAT
GAACCCACGCGTTCCCTAAGCGGCCTCATTCTGAAGAATAATATAAGAATACATGCTTCT
TCATTACAACCTGAAATAATTGAATATATTAAGAAAGAGTGTCTTACGGCTCTCGGTGAC
CCATCTCCGCTGATTCGTGCCACTGTTGGTATATTGATAACGACAATTGCTAATAAAGGT
GGAATCCTTAGTTGGCCAGAGCTGCTTCCAACACTTTGTGAAATGCTTGATTCACATGAA
TATAGTATTTGTGAAGGTGCTTTTGGTGCATTACAAAAGATATGTGAAGATTCTGCTGAA
GTACTTGATAGCAATGAGTTAAATAGACCATTAAACATCATGATACCAAAATTTCTTCAA
TTTTTTCGACATACTAGTCCAAAAATTAGATCGCATGCTATTGCCTGCATAAATCAGTTT
ATAATTCATAGGACGCAAGCGTTAATGATTCATATTGATACATTTATTGAAAATCTTTTT
CACTTATCAAGTGATGAAGATCATGAAGTGAGAAAAAACGTCTGTAGAGGATTAGTGATG
CTATTGGATGTAAGAATGGATCGTTTAATGCCACATATGAATGCTATAATTGAATACATG
TTAGTTAGAACACAAGACCCTGATGAAACGGCTTTAGAAGCTTGCGAATTTTGGCTTTCA
CTTGCAGAACATCCTGTATGTAAAGAAGTTCTTGGTCCTCATTTACATAAATTAGCACCA
GTATTGGTTAAAGGTATGAAGTACTCAGAAATTGACATCATCATTCTGAAGGGAGACGTC
GAAGAGGATGAATTTATTCCAGACAGAGATGAAGACATTAAACCGCGCTTTCATAAATCT
AGAACTCATACATTAAAAGCTGATTTGCATCAAAGCGGAGGAACTGTTGGTAGTGGTG

>g3693.t6 Gene=g3693 Length=359
MTHWEPQPEGLNQIITLLKQSQSTDNQIQRNVQMKLEELNRYPDFNNYLIYVLTKLTTQD
EPTRSLSGLILKNNIRIHASSLQPEIIEYIKKECLTALGDPSPLIRATVGILITTIANKG
GILSWPELLPTLCEMLDSHEYSICEGAFGALQKICEDSAEVLDSNELNRPLNIMIPKFLQ
FFRHTSPKIRSHAIACINQFIIHRTQALMIHIDTFIENLFHLSSDEDHEVRKNVCRGLVM
LLDVRMDRLMPHMNAIIEYMLVRTQDPDETALEACEFWLSLAEHPVCKEVLGPHLHKLAP
VLVKGMKYSEIDIIILKGDVEEDEFIPDRDEDIKPRFHKSRTHTLKADLHQSGGTVGSG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3693.t6 Gene3D G3DSA:1.25.10.10 - 1 345 0.000000
2 g3693.t6 PANTHER PTHR10527:SF21 TRANSPORTIN-1 8 346 0.000000
3 g3693.t6 PANTHER PTHR10527 IMPORTIN BETA 8 346 0.000000
1 g3693.t6 Pfam PF03810 Importin-beta N-terminal domain 33 100 0.000000
7 g3693.t6 ProSiteProfiles PS50166 Importin-beta N-terminal domain profile. 32 100 8.899000
5 g3693.t6 SMART SM00913 IBN_N_2 32 100 0.000096
4 g3693.t6 SUPERFAMILY SSF48371 ARM repeat 1 341 0.000000

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
GO:0006606 protein import into nucleus 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