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.t1 isoform g3693.t1 27479858 27484613
chr_3 g3693 g3693.t1 exon g3693.t1.exon1 27479858 27479965
chr_3 g3693 g3693.t1 cds g3693.t1.CDS1 27479858 27479965
chr_3 g3693 g3693.t1 exon g3693.t1.exon2 27480335 27480509
chr_3 g3693 g3693.t1 cds g3693.t1.CDS2 27480335 27480509
chr_3 g3693 g3693.t1 exon g3693.t1.exon3 27480567 27480642
chr_3 g3693 g3693.t1 cds g3693.t1.CDS3 27480567 27480642
chr_3 g3693 g3693.t1 exon g3693.t1.exon4 27480710 27480977
chr_3 g3693 g3693.t1 cds g3693.t1.CDS4 27480710 27480977
chr_3 g3693 g3693.t1 exon g3693.t1.exon5 27481042 27483021
chr_3 g3693 g3693.t1 cds g3693.t1.CDS5 27481042 27483021
chr_3 g3693 g3693.t1 exon g3693.t1.exon6 27483118 27483256
chr_3 g3693 g3693.t1 cds g3693.t1.CDS6 27483118 27483256
chr_3 g3693 g3693.t1 exon g3693.t1.exon7 27483353 27483375
chr_3 g3693 g3693.t1 cds g3693.t1.CDS7 27483353 27483375
chr_3 g3693 g3693.t1 exon g3693.t1.exon8 27483699 27484378
chr_3 g3693 g3693.t1 cds g3693.t1.CDS8 27483699 27484378
chr_3 g3693 g3693.t1 exon g3693.t1.exon9 27484442 27484613
chr_3 g3693 g3693.t1 cds g3693.t1.CDS9 27484442 27484613
chr_3 g3693 g3693.t1 TSS g3693.t1 27484712 27484712
chr_3 g3693 g3693.t1 TTS g3693.t1 NA NA

Sequences

>g3693.t1 Gene=g3693 Length=3621
ATGCCTGCCGAACTTTCAACCGCAAAAGTAGTAATTCATCCATTGGTTTTGCTATCAGTT
GTCGATCATTTCACTAGAATGAGTAAAATTGGTAATCAAAAGAGAGTTGTTGGTGTTTTG
CTTGGTTGTTGGAAAGCAAAAGGAATTTTAGATGTTTCAAACAGTTTTGCAGTTCCATTT
GATGAAGATGATAAAGATAAAAGTGTTTGGTTCTTGGATCATGATTATCTTGAATCAATG
TATGGTATGTTCAAGAAAGTAAATGCACGTGAAAGAGTTGTTGGCTGGTATCATACGGGA
CCAAAATTACATCAGAATGATATTGCAATTAATGAACTTTTGCGACGCTATTGCCCAAAT
TCAGTGTTAGTTATAATAGATGCTCATCCGAAAGAACTTGGTTTGCCTACTGAAGCATAT
ATTGCAGTTGAAGAGGTTCATGATGATGGAACATTAACTAAAAAAACATTTGAGCATGTC
CCGAGTCAAATTGGTGCAGAAGAAGCTGAAGAAGTTGGTGTTGAACACCTATTACGTGAT
ATCAAAGACACTACTGTTGGAAGTTTGTCACAGAAAGTCACGAATCAACTATTGGGTTTA
AAAGGACTAAATGCGCAACTTCGAGATATTAAAGAGTATCTACTCAAAGTTGGAAATGGA
GAAATGCCCATCAATCATCAAATTATGTATCAAATGCAAGATATTTTCAATCTTCTTCCC
GACATTAGTCATGATAATTTCACCGACACTCTTTATATCAAGACTAACGATCAAATGCTT
GTTGTTTATTTAGCTTCATTGGTTCGATCCATTATTGCTTTACATAATTTAATTAACAAT
AAGCTTACAGAAGACATCACATTAGATAAAAGAAGACATTCGCACCATAATATTTTTCCA
TTTTTACCAAAAATGACACATTGGGAGCCACAACCAGAAGGTTTAAATCAAATAATTACA
CTTCTTAAACAGAGTCAATCGACAGATAATCAAATTCAAAGAAATGTTCAAATGAAATTA
GAAGAATTGAATAGATATCCTGATTTTAACAACTATTTAATTTACGTTCTTACGAAGTTG
ACTACTCAAGATGAACCCACGCGTTCCCTAAGCGGCCTCATTCTGAAGAATAATATAAGA
ATACATGCTTCTTCATTACAACCTGAAATAATTGAATATATTAAGAAAGAGTGTCTTACG
GCTCTCGGTGACCCATCTCCGCTGATTCGTGCCACTGTTGGTATATTGATAACGACAATT
GCTAATAAAGGTGGAATCCTTAGTTGGCCAGAGCTGCTTCCAACACTTTGTGAAATGCTT
GATTCACATGAATATAGTATTTGTGAAGGTGCTTTTGGTGCATTACAAAAGATATGTGAA
GATTCTGCTGAAGTACTTGATAGCAATGAGTTAAATAGACCATTAAACATCATGATACCA
AAATTTCTTCAATTTTTTCGACATACTAGTCCAAAAATTAGATCGCATGCTATTGCCTGC
ATAAATCAGTTTATAATTCATAGGACGCAAGCGTTAATGATTCATATTGATACATTTATT
GAAAATCTTTTTCACTTATCAAGTGATGAAGATCATGAAGTGAGAAAAAACGTCTGTAGA
GGATTAGTGATGCTATTGGATGTAAGAATGGATCGTTTAATGCCACATATGAATGCTATA
ATTGAATACATGTTAGTTAGAACACAAGACCCTGATGAAACGGCTTTAGAAGCTTGCGAA
TTTTGGCTTTCACTTGCAGAACATCCTGTATGTAAAGAAGTTCTTGGTCCTCATTTACAT
AAATTAGCACCAGTATTGGTTAAAGGTATGAAGTACTCAGAAATTGACATCATCATTCTG
AAGGGAGACGTCGAAGAGGATGAATTTATTCCAGACAGAGATGAAGACATTAAACCGCGC
TTTCATAAATCTAGAACTCATACATTAAAAGCTGATTTGCATCAAAGCGGAGGAACTGTT
GGTAGTGGTGGGACAAACGATGATATTGGAGATTCAGATGATGACGATGATGATGGAATA
GTTGATGATTCAAATTTAAGTGATTGGAATTTAAGAAAATGCTCTGCAGCTGCACTAGAC
ATTTTAGCAAATGTCTTTAAAGAGGAAATACTTCCCATATTATTACCTATTCTTAAAGAG
ACTCTATTCCATGAACAATGGGTTATAAAGGAAAGTGGAATTTTAGCACTCGGTGCAATT
GCTGAGGGTTGTATGACAGGAATGATTCCACATCTACCTGAACTAATTCCTTTTTTGATA
AATTGTTTAAGTGATAAGAAGGCCTTAGTGCGATCAATTACTTGTTGGACACTTTCTCGG
TACGCTCATTGGGTCGTATCTCAACCACATGATCAATATTTAAAACCATTGATTGAAGAA
CTTTTGAAAAGGATTCTAGATGCAAATAAAAGAGTTCAAGAAGCAGCATGTTCTGCTTTC
GCAAGTTTGGAAGAAGAAGCCTGTACTGAATTAGTTCCATATCTTGGCTTTATTCTCAAA
ACACTTGTATTTGCGTTTAGCAAGTATCAACATAAAAATCTTCTTATCTTGTATGATGCA
ATCGGAACATTGGCAGATTCAGTTGGACATCATTTGAATAAACCTGAATACATAAGCATG
CTTATGCCACCGCTCATTCAAAAATGGAATATGTTAAAAGATGAAGATAAAGATCTTTTT
CCATTGCTCGAATGTCTTTCTAGTGTTGCCACAGCTCTTCAATCGGGTTTTCTTCCATAT
TGTGAACCAGTCTATCGTCGTTGTATTTCATTAATACAACAAACATTAAATCAAGAAATA
GCCAGCACTACAAGTCCAGCACATTATGAATCACCCGATAAAGATTTTATGATTGTTGCA
CTCGATCTACTGAGTGGCTTAGCTGAAGGATTAGATATACATATTGAGTCGTTAGTAATG
AGCAGTAACATTATGCAACTACTCTATCAATGTATGCAAGATTCTATGCCAGAAGTTCGT
CAGTCATCATTTGCACTTCTTGGAGATTTAACAAAGGCTTGCTTTCAACATGTACATCCA
TACATTTCTGATTTTTTACCTATTCTAGGAAATAATTTAAATCCTGAATACATATCCGTT
TGTAATAACGCAACATGGGCCATTGGTGAAATTAGTATAAAATTAGGTCAAGATACTAAA
TCTTTTATACCCTTAATTTTGCATCAATTGATTGAAATTATTAAGAGTCAAAATACACCG
AAAACTCTTTTGGAAAATACAGCTATTACGATTGGTCGTCTTGGTTTGGTGTGTCCAATT
GAAGTTGCTCCATCGCTTCAACAATTTGTGCGACAATGGTGCTCATCATTACGGAACATT
CGTGATAATGAAGAAAAAGATTCTGCTTTCCGCGGCATGTGTCAAATGATAACAGTTAAT
CCATCAGGAGTGGTGCCTGACTTTATTTTCTTTTGTGATGCAGCAGCATCATGGAGTAAT
CCTAAACCTGACCTACATGAAATGCTTAAAAATATTTTACATGGTTTCAAAACTCAAGTT
GGTGATGATAATTGGCGTCATTTTGTAGATCAATTTCCACCACAGTTAGCTGAGAGGCTT
AATGCTATGTATGACATATAA

>g3693.t1 Gene=g3693 Length=1206
MPAELSTAKVVIHPLVLLSVVDHFTRMSKIGNQKRVVGVLLGCWKAKGILDVSNSFAVPF
DEDDKDKSVWFLDHDYLESMYGMFKKVNARERVVGWYHTGPKLHQNDIAINELLRRYCPN
SVLVIIDAHPKELGLPTEAYIAVEEVHDDGTLTKKTFEHVPSQIGAEEAEEVGVEHLLRD
IKDTTVGSLSQKVTNQLLGLKGLNAQLRDIKEYLLKVGNGEMPINHQIMYQMQDIFNLLP
DISHDNFTDTLYIKTNDQMLVVYLASLVRSIIALHNLINNKLTEDITLDKRRHSHHNIFP
FLPKMTHWEPQPEGLNQIITLLKQSQSTDNQIQRNVQMKLEELNRYPDFNNYLIYVLTKL
TTQDEPTRSLSGLILKNNIRIHASSLQPEIIEYIKKECLTALGDPSPLIRATVGILITTI
ANKGGILSWPELLPTLCEMLDSHEYSICEGAFGALQKICEDSAEVLDSNELNRPLNIMIP
KFLQFFRHTSPKIRSHAIACINQFIIHRTQALMIHIDTFIENLFHLSSDEDHEVRKNVCR
GLVMLLDVRMDRLMPHMNAIIEYMLVRTQDPDETALEACEFWLSLAEHPVCKEVLGPHLH
KLAPVLVKGMKYSEIDIIILKGDVEEDEFIPDRDEDIKPRFHKSRTHTLKADLHQSGGTV
GSGGTNDDIGDSDDDDDDGIVDDSNLSDWNLRKCSAAALDILANVFKEEILPILLPILKE
TLFHEQWVIKESGILALGAIAEGCMTGMIPHLPELIPFLINCLSDKKALVRSITCWTLSR
YAHWVVSQPHDQYLKPLIEELLKRILDANKRVQEAACSAFASLEEEACTELVPYLGFILK
TLVFAFSKYQHKNLLILYDAIGTLADSVGHHLNKPEYISMLMPPLIQKWNMLKDEDKDLF
PLLECLSSVATALQSGFLPYCEPVYRRCISLIQQTLNQEIASTTSPAHYESPDKDFMIVA
LDLLSGLAEGLDIHIESLVMSSNIMQLLYQCMQDSMPEVRQSSFALLGDLTKACFQHVHP
YISDFLPILGNNLNPEYISVCNNATWAIGEISIKLGQDTKSFIPLILHQLIEIIKSQNTP
KTLLENTAITIGRLGLVCPIEVAPSLQQFVRQWCSSLRNIRDNEEKDSAFRGMCQMITVN
PSGVVPDFIFFCDAAASWSNPKPDLHEMLKNILHGFKTQVGDDNWRHFVDQFPPQLAERL
NAMYDI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3693.t1 CDD cd08062 MPN_RPN7_8 9 282 5.76441E-172
11 g3693.t1 Coils Coil Coil 798 818 -
8 g3693.t1 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase 3 187 8.1E-71
10 g3693.t1 Gene3D G3DSA:1.25.10.10 - 305 649 5.1E-124
9 g3693.t1 Gene3D G3DSA:1.25.10.10 - 663 1206 3.3E-262
15 g3693.t1 MobiDBLite mobidb-lite consensus disorder prediction 652 677 -
16 g3693.t1 MobiDBLite mobidb-lite consensus disorder prediction 652 666 -
5 g3693.t1 PANTHER PTHR10527:SF21 TRANSPORTIN-1 311 1204 0.0
6 g3693.t1 PANTHER PTHR10527 IMPORTIN BETA 311 1204 0.0
3 g3693.t1 Pfam PF01398 JAB1/Mov34/MPN/PAD-1 ubiquitin protease 8 120 4.3E-32
2 g3693.t1 Pfam PF13012 Maintenance of mitochondrial structure and function 168 279 6.9E-32
4 g3693.t1 Pfam PF03810 Importin-beta N-terminal domain 337 404 3.0E-13
1 g3693.t1 Pfam PF13513 HEAT-like repeat 727 780 2.3E-12
18 g3693.t1 ProSiteProfiles PS50249 MPN domain profile. 10 146 19.323
17 g3693.t1 ProSiteProfiles PS50166 Importin-beta N-terminal domain profile. 336 404 8.899
14 g3693.t1 SMART SM00232 pad1_6 9 145 2.2E-34
13 g3693.t1 SMART SM00913 IBN_N_2 336 404 9.6E-5
7 g3693.t1 SUPERFAMILY SSF48371 ARM repeat 305 1194 5.04E-195

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:0008237 metallopeptidase activity MF
GO:0005515 protein binding MF
GO:0006606 protein import into nucleus BP
GO:0005838 proteasome regulatory particle CC
GO:0070122 isopeptidase activity MF

KEGG

Orthology

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.

Raw TPM values