General information for g12718.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Importin subunit alpha-4.
Parent gene
- The parent gene g12718 is located on chr_1: 25443485..25444655 (- 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 | g12718 | g12718.t1 | TTS | g12718.t1 | 25442002 | 25442002 |
| chr_1 | g12718 | g12718.t1 | isoform | g12718.t1 | 25442717 | 25444655 |
| chr_1 | g12718 | g12718.t1 | exon | g12718.t1.exon1 | 25442717 | 25442986 |
| chr_1 | g12718 | g12718.t1 | cds | g12718.t1.CDS1 | 25442717 | 25442986 |
| chr_1 | g12718 | g12718.t1 | exon | g12718.t1.exon2 | 25443042 | 25443872 |
| chr_1 | g12718 | g12718.t1 | cds | g12718.t1.CDS2 | 25443042 | 25443872 |
| chr_1 | g12718 | g12718.t1 | exon | g12718.t1.exon3 | 25443931 | 25444161 |
| chr_1 | g12718 | g12718.t1 | cds | g12718.t1.CDS3 | 25443931 | 25444161 |
| chr_1 | g12718 | g12718.t1 | exon | g12718.t1.exon4 | 25444388 | 25444528 |
| chr_1 | g12718 | g12718.t1 | cds | g12718.t1.CDS4 | 25444388 | 25444528 |
| chr_1 | g12718 | g12718.t1 | exon | g12718.t1.exon5 | 25444605 | 25444655 |
| chr_1 | g12718 | g12718.t1 | cds | g12718.t1.CDS5 | 25444605 | 25444655 |
| chr_1 | g12718 | g12718.t1 | TSS | g12718.t1 | 25444831 | 25444831 |
Sequences
>g12718.t1 Gene=g12718 Length=1524
ATGGAGAATCATCGAAATAATTTATTTAAAAATAAAGGAAAAGATCAAGATGAGATGAGA
AGAAGGAGAACTGAAGTCTCAATTGAACTACGTAAAAACAAAAGAGAAGATACAATTCAA
AAACGCAGAAATATTTATCAGTCAGAAACTTCCGACGATGATCTATTATCTGTTCCCAAT
TTGAAAAAACTGGTAATGTCTGCAGGTAATGATGGTGATCCTGAAGATCAATTACAAGCA
GTACAAACAGCACGTCGTTTACTCTCGTCTGACCGCAATCCGCCTATTGATGAGTTGATA
AAAAGTGGAATCTTGCCAATTCTTGTACGTTGTTTAGAACGCGATGAAAATCAGATGTTG
CAATTCGAAGCAGCATGGGCTTTAACAAATATTGCATCCGGCACATCACAACAGACTAAT
TTAGTAGTTAATGCTGGAGCTGTTCCATTATTTATTCGACTTTTAATGTCACCAGCAGCA
AATGTTTGTGAACAAGCAGTTTGGGCATTGGGAAATATTATTGGTGATGGGCCACAATTG
CGAGATTATGTTATAAAATTGGGAGTTGTACAGCCATTACTATCGTTTGTGAAGCCCGAT
ATTCCAATCAGTTTTCTTCGTAATGTAACATGGGTAATTGTCAATTTATGCCGCAACAAA
GATCCACCACCACCAATTCAAACAATCAATCAAATTCTTCCGGCACTTTGTCATCTTATT
CACAATCCAGATGTCAATATTCTCGTCGATACTGTATGGGCTTTGAGTTATTTAACGGAT
GGTGGAAATGAACAAATTCAATTGGTCATCGATAGTGGTGTTGTTCCGCATTTGATTCCA
TTATTATCACATGTTGAAGTAAAGGTACAAACTGCTGCTCTTCGTGCTGTAGGCAATATA
GTTACAGGATCAGATGAGCAGACGCAAGTTGTACTCAATTATAATGCATTATCACATTTT
CCGGCCCTCTTGAGTCATCCCAAAGAGAAAATTCGCAAAGAGGCAGTGTGGTTTTTGTCT
AATATCACAGCTGGTGTACAAACACAAGTTCAAGCGGTCATTGATGCAGGTTTATTGCCG
AAAATTATTGAAAATTTGTCAAAAGGAGAATTTCAGACGCAGAAAGAAGCTGCTTGGGCA
ATCAGTAATTTGACGATCAGTGGCAATAAGGAGCAAGTGGCAGAATTAATCAAAGCAGGA
GCAATTCCACCTTTCTGCGAATTACTAAGATGTCATGATACTCAAGTTATCAATGTAATT
TTGGATGGTATCAATAATATGCTAAAAATGGCAGGTCCAAATGCAGAACAAATTGCTATG
CTAATAGAAGAATGCGATGGTTTAACGAAAATCGAGGATCTGCAAAATCATGAGAATGTC
GAAATTTATAAGCTGGCATATGATATTATTGAGCAGTACTTTAGCGATGAAGTTGGCGAA
GATGATGCTGGTATTAATCCACAAGTAGATGACGGTGGCAACTTCCAATTTAATCCAAAT
CAAAATCTTGAATTCAACTTTTAA
>g12718.t1 Gene=g12718 Length=507
MENHRNNLFKNKGKDQDEMRRRRTEVSIELRKNKREDTIQKRRNIYQSETSDDDLLSVPN
LKKLVMSAGNDGDPEDQLQAVQTARRLLSSDRNPPIDELIKSGILPILVRCLERDENQML
QFEAAWALTNIASGTSQQTNLVVNAGAVPLFIRLLMSPAANVCEQAVWALGNIIGDGPQL
RDYVIKLGVVQPLLSFVKPDIPISFLRNVTWVIVNLCRNKDPPPPIQTINQILPALCHLI
HNPDVNILVDTVWALSYLTDGGNEQIQLVIDSGVVPHLIPLLSHVEVKVQTAALRAVGNI
VTGSDEQTQVVLNYNALSHFPALLSHPKEKIRKEAVWFLSNITAGVQTQVQAVIDAGLLP
KIIENLSKGEFQTQKEAAWAISNLTISGNKEQVAELIKAGAIPPFCELLRCHDTQVINVI
LDGINNMLKMAGPNAEQIAMLIEECDGLTKIEDLQNHENVEIYKLAYDIIEQYFSDEVGE
DDAGINPQVDDGGNFQFNPNQNLEFNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g12718.t1 | Gene3D | G3DSA:1.20.5.690 | Single helix bin | 4 | 45 | 5.1E-18 |
| 14 | g12718.t1 | Gene3D | G3DSA:1.25.10.10 | - | 58 | 476 | 9.2E-187 |
| 25 | g12718.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 11 | g12718.t1 | PANTHER | PTHR23316 | IMPORTIN ALPHA | 3 | 497 | 1.3E-255 |
| 12 | g12718.t1 | PANTHER | PTHR23316:SF28 | IMPORTIN SUBUNIT ALPHA | 3 | 497 | 1.3E-255 |
| 16 | g12718.t1 | PIRSF | PIRSF005673 | Importin_alpha | 1 | 507 | 1.6E-208 |
| 1 | g12718.t1 | Pfam | PF01749 | Importin beta binding domain | 5 | 82 | 9.2E-18 |
| 8 | g12718.t1 | Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 93 | 133 | 4.1E-12 |
| 7 | g12718.t1 | Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 136 | 173 | 2.5E-11 |
| 5 | g12718.t1 | Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 178 | 218 | 4.0E-6 |
| 6 | g12718.t1 | Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 222 | 259 | 1.7E-6 |
| 4 | g12718.t1 | Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 263 | 301 | 4.6E-11 |
| 3 | g12718.t1 | Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 304 | 344 | 1.6E-9 |
| 9 | g12718.t1 | Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 349 | 385 | 1.0E-8 |
| 10 | g12718.t1 | Pfam | PF00514 | Armadillo/beta-catenin-like repeat | 389 | 427 | 1.3E-5 |
| 2 | g12718.t1 | Pfam | PF16186 | Atypical Arm repeat | 436 | 487 | 2.8E-22 |
| 26 | g12718.t1 | ProSiteProfiles | PS51214 | IBB domain profile. | 1 | 52 | 15.795 |
| 28 | g12718.t1 | ProSiteProfiles | PS50176 | Armadillo/plakoglobin ARM repeat profile. | 103 | 146 | 10.272 |
| 27 | g12718.t1 | ProSiteProfiles | PS50176 | Armadillo/plakoglobin ARM repeat profile. | 146 | 173 | 9.432 |
| 24 | g12718.t1 | SMART | SM00185 | arm_5 | 92 | 133 | 5.6E-10 |
| 18 | g12718.t1 | SMART | SM00185 | arm_5 | 135 | 175 | 2.5E-7 |
| 20 | g12718.t1 | SMART | SM00185 | arm_5 | 177 | 218 | 5.5 |
| 22 | g12718.t1 | SMART | SM00185 | arm_5 | 221 | 260 | 0.0015 |
| 19 | g12718.t1 | SMART | SM00185 | arm_5 | 262 | 302 | 1.4E-8 |
| 17 | g12718.t1 | SMART | SM00185 | arm_5 | 304 | 344 | 2.4E-7 |
| 21 | g12718.t1 | SMART | SM00185 | arm_5 | 345 | 386 | 2.4E-4 |
| 23 | g12718.t1 | SMART | SM00185 | arm_5 | 389 | 429 | 5.1E-4 |
| 13 | g12718.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 3 | 477 | 7.68E-125 |
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:0005515 | protein binding | MF |
| GO:0061608 | nuclear import signal receptor activity | MF |
| GO:0006606 | protein import into nucleus | BP |
| GO:0005737 | cytoplasm | CC |
KEGG
Orthology
- This transcript has been annotated with K23583 (importin subunit alpha-4/3)
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.
