Gene loci information

Transcript annotation

  • This transcript has been annotated as Importin subunit beta-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_2 g5619 g5619.t4 isoform g5619.t4 10655563 10657094
chr_2 g5619 g5619.t4 exon g5619.t4.exon1 10655563 10656321
chr_2 g5619 g5619.t4 cds g5619.t4.CDS1 10655609 10656321
chr_2 g5619 g5619.t4 exon g5619.t4.exon2 10656410 10657094
chr_2 g5619 g5619.t4 cds g5619.t4.CDS2 10656410 10656485
chr_2 g5619 g5619.t4 TTS g5619.t4 10657086 10657086
chr_2 g5619 g5619.t4 TSS g5619.t4 NA NA

Sequences

>g5619.t4 Gene=g5619 Length=1444
TGTATCAACTCTGTGCGATTTATTAAACGAAGGTTTTATCAAATACATGGAAGCATTTAA
ACCATTCTTGTATATGGCACTAAGAAATCATCAAGATTATCAAGTCTGCTCTGTTGCCAT
TGGTTTAGTTGGTGACATTGCTCGTGCACTCAAACTTGCTGTCATTCCATATTGCGATGA
AATTATGAGTATGCTCATGCAAAATTTAAGCAATCCCGAAATACATCGTGATGTTAAACC
ACAAGTTTTAAGTGTCTTTGGTGACATTGCTCTCAGCATAAGTGGAGAATTTAAGAAATA
TCTCGAGCCAGTTTTAGATGTTCTTACTCAAGTGATGGGTCTTCAAGTTGAACAAAAAGA
TTTTGAAATGCGTGACTATTTCTGTGTTTTACGTGAAAGTGTTTTAGAAGCTTACACAGG
AATCGTTCAAGGATTAAAGGGGCCAGATCCAAATAAAGTTCATCCAGATATTATGCTTCT
CCAAAATCACGTTCCACTTATCGTCAAATATATCGTTCAAACAGCTCAAGATCCTGATCT
TTCTGAAAGTACAATGACTAGCTGTGCTGGTTTAATAGGCGATTTATGTGCTGCTTTTGG
TGCACCACTTTTACCATATTTACTCGAAGACAATATCGTTATGCCAATGCTTACGGAAGG
AAAGAAATCACAAGCATCACGTACAAAGTCTACTTGCAGTTGGGCGCTTCGTGCTATCAA
AACATTAAAACAATCATCTCAACTCGCGCCTGCCGTTAATAATGTTGCACAACCACCTAC
AGCTAACAATAACAACAACATTCAATTTACCAATAACTTTCCAAATGCTGTTTAGAGCTA
TAGAAGAAATGAATACTATAATGAATTGTCAACCGATGAAATATGGTCAGTAAGTAAGAT
TCATCAGCAACATTGTAATTCACATATGTTCTAGTAGATATGATGCACACTATTGAAAGT
TTTTTTTGTAAATCTACTTTATAATGAATTCTTTTACCAACACGACCCCTGACCCTTGCT
TAATTGTATACATCTTTTATCATAACATTATAATTATTATTTAAGTCAAAGTGGAATTTT
TCTTCCAAATGCTCGTTTGTTGCCTGTCCCTTATTCCTTATAATTTTTCAATACAATTTT
TCCATGAAAACTAAGAATCTAAGCTTTATTACTTCACTCGTTCATTTATCTGATCGATTA
GAGATATTCCACTTATAATCTTCAAAATCAAGAAAGTTTCTCTTCTGACCTAAACATTTT
TTTTTAAATATGAAATTCTTTTTTAATTAATTTATGTCGCGCACTATTTTAATAAAAAAT
ACATAAAAACTTCAATTATTTTGTAATGTGGAATTTTCTATTTTTGCTTATCCACATATG
AATATGATTTAATAAGAAACACAAAATTACTAGTTTAAGAAATATAAAAAATGAAGAAAA
AAAA

>g5619.t4 Gene=g5619 Length=262
MEAFKPFLYMALRNHQDYQVCSVAIGLVGDIARALKLAVIPYCDEIMSMLMQNLSNPEIH
RDVKPQVLSVFGDIALSISGEFKKYLEPVLDVLTQVMGLQVEQKDFEMRDYFCVLRESVL
EAYTGIVQGLKGPDPNKVHPDIMLLQNHVPLIVKYIVQTAQDPDLSESTMTSCAGLIGDL
CAAFGAPLLPYLLEDNIVMPMLTEGKKSQASRTKSTCSWALRAIKTLKQSSQLAPAVNNV
AQPPTANNNNNIQFTNNFPNAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g5619.t4 Gene3D G3DSA:1.25.10.10 - 1 240 0
1 g5619.t4 PANTHER PTHR10527 IMPORTIN BETA 1 226 0
2 g5619.t4 PANTHER PTHR10527:SF1 IMPORTIN SUBUNIT BETA-1 1 226 0
3 g5619.t4 SUPERFAMILY SSF48371 ARM repeat 3 225 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5619/g5619.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5619.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
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.

Raw TPM values