General information for g5619.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Importin subunit beta.
Parent gene
- The parent gene g5619 is located on chr_2: 10655563..10657094 (+ 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_2 | g5619 | g5619.t2 | TSS | g5619.t2 | 10652337 | 10652337 |
| chr_2 | g5619 | g5619.t2 | isoform | g5619.t2 | 10653069 | 10654789 |
| chr_2 | g5619 | g5619.t2 | exon | g5619.t2.exon1 | 10653069 | 10653114 |
| chr_2 | g5619 | g5619.t2 | cds | g5619.t2.CDS1 | 10653069 | 10653114 |
| chr_2 | g5619 | g5619.t2 | exon | g5619.t2.exon2 | 10653654 | 10653895 |
| chr_2 | g5619 | g5619.t2 | cds | g5619.t2.CDS2 | 10653654 | 10653895 |
| chr_2 | g5619 | g5619.t2 | exon | g5619.t2.exon3 | 10653959 | 10654789 |
| chr_2 | g5619 | g5619.t2 | cds | g5619.t2.CDS3 | 10653959 | 10654789 |
| chr_2 | g5619 | g5619.t2 | TTS | g5619.t2 | NA | NA |
Sequences
>g5619.t2 Gene=g5619 Length=1119
ATGACTATGGAACTAATTAATATATTGGAAAAAACTGTTTCATCAGATAAAAATGAGCTT
GAAGCAGCACAACAATTTTTGGAGCATGCCGCTTCTAACAATCATCCTGACTTTCTTAAA
GCACTTTCGGACGTTCTATGTCATCCTGGAAATTCGCCTGTATCAAGAATGGCGGCTGGT
TTACAATTAAAAAATCAATTGACTAGCAAAGATGAATCTGTGAAGCAAAAATTTCAATCA
AAATGGCTACAGTTACCAGAAGAAATCAGAAGTTATGTAAAGAAAAATATTTTGAGTGCA
CTTGGTACCGAAAGTTTAAGACCATCTTCAGCTGCTCAATGTGTGGCTTATGTCGCAGTT
ACAGAACTTCCTCATGGACAATGGCCAGATCTCATACAAATGCTTGTTGGTAATGTCATC
AATGAGCGATCTACAGAAATGGAACGTGAAGCAACATTGGAAACAATTGGCTACATTTGT
CAAGATATCAATTCTGATATTTTGGAACCACAATCAAATGCAATTCTCACCGCTATTATT
CATGGAATGCGAAAAAATGAATCAAGTAATCACGTTAGATTGGCAGCAACTAATGCTCTT
TTAAACTCGCTAGAATTTACCAAAGCCAATTTTGAAAAGGAGTCTGAGAGAAATTTTATC
ATGGAAGTCGTATGTGAAGCAACACAGAGTGTAGACATTCAAATAAGCGTTGCTGCTTTG
CAGTGTTTAGTGAAAATTATGACACTTTATTATCAATTTATGGAACCTTATATGGCTCAA
GCACTTTTCCCAATTACACTAGAAGCAATGAAATCTGAAAACGATCAAGTTGCACTTCAA
GGTATTGAATTTTGGTCTAATGTATGCGATGAAGAAATTGATCTTGCCATTGAATCACAA
GAAGCGAAAAATGCAGGACAAACACCAGAACATGTGTCTAGACATTATGCTCGTGGTGCT
CTGCAATATCTTGCACCAGTATTGATGCAGAAATTAACCAATCAAGAAGAGAACGATGAT
GACGACGATTGGAATCCATCAAAATCTGCAAGTGTTTGTCTCATGTTGTTGGCGACCTGC
TGCGAAGATGATATCGTTCCACATGTTCTTCCATTCATA
>g5619.t2 Gene=g5619 Length=373
MTMELINILEKTVSSDKNELEAAQQFLEHAASNNHPDFLKALSDVLCHPGNSPVSRMAAG
LQLKNQLTSKDESVKQKFQSKWLQLPEEIRSYVKKNILSALGTESLRPSSAAQCVAYVAV
TELPHGQWPDLIQMLVGNVINERSTEMEREATLETIGYICQDINSDILEPQSNAILTAII
HGMRKNESSNHVRLAATNALLNSLEFTKANFEKESERNFIMEVVCEATQSVDIQISVAAL
QCLVKIMTLYYQFMEPYMAQALFPITLEAMKSENDQVALQGIEFWSNVCDEEIDLAIESQ
EAKNAGQTPEHVSRHYARGALQYLAPVLMQKLTNQEENDDDDDWNPSKSASVCLMLLATC
CEDDIVPHVLPFI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5619.t2 | Gene3D | G3DSA:1.25.10.10 | - | 1 | 373 | 0.0000000 |
| 2 | g5619.t2 | PANTHER | PTHR10527 | IMPORTIN BETA | 5 | 373 | 0.0000000 |
| 3 | g5619.t2 | PANTHER | PTHR10527:SF1 | IMPORTIN SUBUNIT BETA-1 | 5 | 373 | 0.0000000 |
| 1 | g5619.t2 | Pfam | PF03810 | Importin-beta N-terminal domain | 23 | 103 | 0.0000000 |
| 7 | g5619.t2 | ProSiteProfiles | PS50166 | Importin-beta N-terminal domain profile. | 23 | 103 | 19.8890000 |
| 5 | g5619.t2 | SMART | SM00913 | IBN_N_2 | 23 | 103 | 0.0000001 |
| 4 | g5619.t2 | SUPERFAMILY | SSF48371 | ARM repeat | 3 | 373 | 0.0000000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5619/g5619.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5619.t2.fa.iupred3.txt does not exist
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.
