General information for g12900.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g12900.t1 | 26785935 | 26785935 |
| chr_1 | g12900 | g12900.t1 | isoform | g12900.t1 | 26786061 | 26789033 |
| chr_1 | g12900 | g12900.t1 | exon | g12900.t1.exon1 | 26786061 | 26786124 |
| chr_1 | g12900 | g12900.t1 | cds | g12900.t1.CDS1 | 26786061 | 26786124 |
| chr_1 | g12900 | g12900.t1 | exon | g12900.t1.exon2 | 26786189 | 26787687 |
| chr_1 | g12900 | g12900.t1 | cds | g12900.t1.CDS2 | 26786189 | 26787687 |
| chr_1 | g12900 | g12900.t1 | exon | g12900.t1.exon3 | 26787765 | 26788856 |
| chr_1 | g12900 | g12900.t1 | cds | g12900.t1.CDS3 | 26787765 | 26788856 |
| chr_1 | g12900 | g12900.t1 | exon | g12900.t1.exon4 | 26788917 | 26789033 |
| chr_1 | g12900 | g12900.t1 | cds | g12900.t1.CDS4 | 26788917 | 26789033 |
| chr_1 | g12900 | g12900.t1 | TSS | g12900.t1 | 26789187 | 26789187 |
Sequences
>g12900.t1 Gene=g12900 Length=2772
ATGGAAGAGGAACCTAAAATTGAAGACGTTTTAAATAAAATTTACGATTTATACTGTAAT
CCTGACATTTCTAAAAAAGATCCTGCATCAAAGTATCTTGCAAGCCTACAAGATTCGATT
TATTCATGGAAAATCTCGGATCAATTATTACAGCAAAAGAATGATATGCATTCATGCTAT
TATGCCGCACAGACACTTCGAAGTAAGATACAACACTCATTTCATGAGCTACATGAGTCT
GACTACATTTCTCTACGTGATTCAATTATTGCTCATATAGAGCATATTACGCCAGATACA
AATCCAACGATAGCAAAACAATTATGTTTAGCATTAGCAGATCTATTGCTTTTGATGGCA
TCTTGGATGAAGCCAGTAGATGATTTAATTAAGAAATTCTCACAGAAAACTGATTCCATC
CAACCGCTATTGATGTTGCTAACATTTATACCAGAAGAACTTGATGCTCGATATTTAAGA
ATTGGTGAAAATCGAAGAAAACAAATTCTTAATGAACTCGACACTAGTTCACCTATAATA
CTCAGTTTTCTTCAATCATGCTTGATGATTAACGATACATCTATCCTTCAACATATTTAT
GTCGATGTAATTCAATGCTTTACGGCATGGGTTAAAATGGATTGCATAAATCTAACTGAT
GCGGCTGTTTCTCCAGTGTTTTCTTATGCTTTTAAAATTCTTACTAGTCCTCCTTCAACG
ACCGATGAAAAACAATTGGAAGTTGCTTCTGACTGTGTTTGTGCTATTTTAGAGGCAATT
GTACTAGAGCGTACCACTGAAGAAATCGAGAAAAATATATTTCTAGGAGTTTTGCAATTG
GAACATGCTTATAATGAAGCAGTAGCACAAGAAGATGTCGATAAATGTATGGTTCTTTGT
CGAATTTTTACTGTAATGGCAGAAACCTTTTTGCCGCGTATTGTTAATTCGAGTACACCA
TCAAATCCACATTATACAATCAAAGCTCTTGATGTATTGATTATGTGTGTAGGACATTAT
GATTTTGAGCTCGCTCAAATAACATTTTCTGTATGGTATAAACTTAGTGAAGAATTATAT
CAAAAAAATGACGATAATCATACGGCAATATTTGAAAACCATATTGAGAGATTGATCGAG
GCACTTTTCAAACATTGTCAATTGGACGCTGATCATGAAGGATTGATTAATGAAGAAGAT
ACATTTGGTGAATTTCGATACAAAGTATCTGAACTGATAAAAGACGTTTCGTTCATAGTG
CGAAGTAAAAGTTGTTTTCAACACATGTTTAATGTTCTTCAAAATCCTAATGTGACATGG
GAAGCAACTGAAGCAGCTTTGTTCATAATGGAGTGTGTTGCACGCAATCTTGACGTTAAA
GAAGACAAAATAGTCCCAAAAGTTCTTGAAGCTATTTTAAATTTACCCGATAGTTGTCAT
GTTGCAATTCGTTTTACATCTGTGAATATGTTAGGACAATTATGCGATTGGATTTCTGCT
CATCCTACAACATTAGAAGCCGTTTTAAATTTTCTACTTGGAGCACTTCAAAAGAAAGCA
GGACTCGCTTCAGCTGCCGCTCAATCTTTGCAATTGATTTGCTCTTCATGCCATAAAGAT
ATGATAAATCACATTAGTGGATTGTTGGAAATAGCAAGATGCTTAGAAATGTTTGAAGTT
CAACCTAATGCAGCCATAGCATTATTGAAGGGAATTTCTCAAACTGTCAGTCGCTTACCA
AATGATCAAATCACTGAAGTAATGCGACAATTATGCGCTTTTCAAATAGCACATCTGTGT
ATGCTCATGGAAAATGAGGATAAAAAAGACCCAACACAATGGATTGATCGATTAGCGGCA
ATCTATCGATATATGAATCCAAGAGTGTGTGAAAATGAACCAAATCCAGCAACAGCAGTG
ATAATAGAAAATTGGCCAGTACTCTCAAGAATGCTCGATTATTATAAGCAAAACGAGAAA
ATTATCGAAAGGATTGTTAGATGCATTCGTTATGGTATTCGCTGTATATCACACGAATCT
TTGCCAATATTAGATTCTTTAGTCACGCAAATGGTCAATGTCTATTCTTCACAAAAGCAT
AGCTGTTTATTGTATCTTGGTAGTATTCTAGTCGATGAATTTGGAAATGATGTACGATGT
ATCAGTGGTCTATTAAGTATGCTTGAGGCTTTTATAGAACCAACATTCAATCTCCTTCAA
ACTGAAAATGGACTGAAAAATAATCCTGATACAGTTGATGATTTCTTCAGAATTGTTGTA
AGATTTATTCAACGTATGCCATTACAATTTTTACAAAGTCAACTCGTTACACCGATTATT
CAATGTGCAACATTAGCATGTTCTCTTGATCATCGAGATGCAAATATGTCAGTTATGAAA
TTTCTATCAAATTTACTTGTTCACGGAAAAATCAATGGTGATGCTACAATAAGACCATTT
GTCCAAAATATTGTGCAAGCTCATGGTGAAACTCTTATTGTGAATCTTATCTATTCGTCC
GTTTTCTACCTTCATCCAAATATGCTTGCTGATGTAGTAGATGTATTGATGGAAATTAAA
TTCATAAGTAATGAAATTTTTGCCGATGCATTGAAAAAAGCTCTTAACCAATTGCCAAGA
AAGAACGCTGGTGGCTCTGAAACAGCAACCGAAGAACAATTGAGTAAATTTTTCCAAAAT
ATTACCAAAACAAATATTAGTGTACGTCAAATGACTCATGAGCTTCAAGACTTTTGTCGA
CTTTTCAGATAA
>g12900.t1 Gene=g12900 Length=923
MEEEPKIEDVLNKIYDLYCNPDISKKDPASKYLASLQDSIYSWKISDQLLQQKNDMHSCY
YAAQTLRSKIQHSFHELHESDYISLRDSIIAHIEHITPDTNPTIAKQLCLALADLLLLMA
SWMKPVDDLIKKFSQKTDSIQPLLMLLTFIPEELDARYLRIGENRRKQILNELDTSSPII
LSFLQSCLMINDTSILQHIYVDVIQCFTAWVKMDCINLTDAAVSPVFSYAFKILTSPPST
TDEKQLEVASDCVCAILEAIVLERTTEEIEKNIFLGVLQLEHAYNEAVAQEDVDKCMVLC
RIFTVMAETFLPRIVNSSTPSNPHYTIKALDVLIMCVGHYDFELAQITFSVWYKLSEELY
QKNDDNHTAIFENHIERLIEALFKHCQLDADHEGLINEEDTFGEFRYKVSELIKDVSFIV
RSKSCFQHMFNVLQNPNVTWEATEAALFIMECVARNLDVKEDKIVPKVLEAILNLPDSCH
VAIRFTSVNMLGQLCDWISAHPTTLEAVLNFLLGALQKKAGLASAAAQSLQLICSSCHKD
MINHISGLLEIARCLEMFEVQPNAAIALLKGISQTVSRLPNDQITEVMRQLCAFQIAHLC
MLMENEDKKDPTQWIDRLAAIYRYMNPRVCENEPNPATAVIIENWPVLSRMLDYYKQNEK
IIERIVRCIRYGIRCISHESLPILDSLVTQMVNVYSSQKHSCLLYLGSILVDEFGNDVRC
ISGLLSMLEAFIEPTFNLLQTENGLKNNPDTVDDFFRIVVRFIQRMPLQFLQSQLVTPII
QCATLACSLDHRDANMSVMKFLSNLLVHGKINGDATIRPFVQNIVQAHGETLIVNLIYSS
VFYLHPNMLADVVDVLMEIKFISNEIFADALKKALNQLPRKNAGGSETATEEQLSKFFQN
ITKTNISVRQMTHELQDFCRLFR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12900.t1 | Gene3D | G3DSA:1.25.10.10 | - | 2 | 923 | 0.0e+00 |
| 3 | g12900.t1 | PANTHER | PTHR12363:SF42 | TRANSPORTIN-3 | 1 | 895 | 0.0e+00 |
| 4 | g12900.t1 | PANTHER | PTHR12363 | TRANSPORTIN 3 AND IMPORTIN 13 | 1 | 895 | 0.0e+00 |
| 1 | g12900.t1 | Pfam | PF03810 | Importin-beta N-terminal domain | 29 | 93 | 2.3e-05 |
| 2 | g12900.t1 | Pfam | PF08389 | Exportin 1-like protein | 103 | 239 | 0.0e+00 |
| 5 | g12900.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 1 | 907 | 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 transcript has been annotated with K15436 (transportin-3)
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.
