General information for g5478.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AP-1 complex subunit gamma-1.
Parent gene
- The parent gene g5478 is located on chr_2: 9810267..9819560 (- 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 | g5478 | g5478.t2 | TTS | g5478.t2 | 9805274 | 9805274 |
| chr_2 | g5478 | g5478.t2 | isoform | g5478.t2 | 9805787 | 9810267 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon1 | 9805787 | 9805879 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS1 | 9805787 | 9805879 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon2 | 9805939 | 9806049 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS2 | 9805939 | 9806049 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon3 | 9806112 | 9806850 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS3 | 9806112 | 9806850 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon4 | 9806912 | 9807053 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS4 | 9806912 | 9807053 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon5 | 9807123 | 9807543 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS5 | 9807123 | 9807543 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon6 | 9807608 | 9808030 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS6 | 9807608 | 9808030 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon7 | 9808725 | 9808801 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS7 | 9808725 | 9808801 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon8 | 9808862 | 9809100 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS8 | 9808862 | 9809100 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon9 | 9809166 | 9809496 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS9 | 9809166 | 9809496 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon10 | 9809628 | 9809695 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS10 | 9809628 | 9809695 |
| chr_2 | g5478 | g5478.t2 | exon | g5478.t2.exon11 | 9810251 | 9810267 |
| chr_2 | g5478 | g5478.t2 | cds | g5478.t2.CDS11 | 9810251 | 9810267 |
| chr_2 | g5478 | g5478.t2 | TSS | g5478.t2 | 9811058 | 9811058 |
Sequences
>g5478.t2 Gene=g5478 Length=2661
ATGAATACAGATAGCGGATTTAATCCTGGCTTAAACATGGCCACAATTCGTCAAGCGATA
AATGAGACAATTGAAAGGGGTATAATGCGTATGCCTACACCAACGAGACTTAGAGATCTG
ATTCGTCAAATTCGTGCTGCAAAAACACAAGCAGAAGAACGAGCTGTTGTAAATCGAGAA
TGTGCCTATATTCGATCGACATTCAGAGAAGAAGATTCCGTTTGGCGATGCAGGAATATA
GCAAAACTTTTTTACATTCATATGCTAGGATATCCAGCACACTTTGGACAACTTGAGTGT
CTAAAACTAATTGCAAGTCCTAAATTTACTGATAAGCGTATTGGATATTTAGGTGCAATG
CTTTTACTGGATGAGCGTCAAGATGTTCATTTGCTCATAACAAACTGCTTAAAAAATGAC
CTTAATAGTCCAACACAATTTGTTGTTGGTTTAGCGCTTTGTACTCTTGGTGCAATTGCA
TCTCCTGAAATGGCGAGGGATTTAGCAGGAGAAATTGAGAAATTAATGAAGTCACCAAAT
GCGTATATTCGAAAAAAGGCCATTCTTTGCGCTTTCAGAATAATTCGTCGTGTGCCTGAA
CTAATGGAAATATTTCTACCTGCTACACGATCGTTGTTAAATGAGAAAAATCATGGGATA
CTCATAACTGGTGTTACGCTAATCACTGAAATGTGTGAAAATAGTCCAGACACATTAAAT
CATTTTAAAAAGATTGTTCCAAATTTAGTACGCATTTTGAAAAATCTAATTCTTGCTGGT
TATTCTCCCGAACACGATGTAAGTGGAGTATCTGATCCATTTTTACAAGTAAAAATTTTA
CGATTGTTGAGAATTCTTGGGCGAAATGATCCTGAAGCATCGGAAGCGATGAATGACATT
CTTGCACAAGTTGCAACAAATACTGAAACAAGTAAAAATGTTGGAAATACGATCTTATAT
GAAACTGTTCTTACTATAATGGATATAAAATCAGAGGGTGGATTACGAGTGCTCGCAGTT
AATATACTTGGAAGATTTTTATTAAATAATGATAAAAATATTCGTTACATAGCATTGCAT
ACACTGTTAAAAACAGTAAATGTAGATATATCTGCAGTTCAACGCCATCGTAGTACGATT
CTCGAATGTTTGAAGGATCCTGATGTTACTATTCGAAAACGAGCAATCGAGTTATCATTT
GCATTAGTAAATGCTCAAAATATAAGAGCAATGGCTAAAGAATTGTTGATATTTTTAGAA
AAAGCAGATCCTGAATTTAAAGCTCAGTGTAGTTCAAGCATGGTATTGTCAGCAGAACGA
TATGCTCCAACTATACGTTGGCATTTAGATACACTTTTAAGTGTTCTTATAGCAGCAGGA
AATTATGTACGTGATGATGTCACTTCATCTACTATTCAAATGATTTCTAGTAGTCCAGCA
AACGAACAGACGTACATTACTGTAAAATTTTGGGATGCAATTCAAGAAACACAAGACAAT
CAACCTCTTTTACAAGTAGCCGTGTGGTGTATTGGAGAATATGGGGATCAAATTCTTTAC
GATTCTGAATTGGAATTTACAAATGAAAGACCTACGGAATCAACAATTATTGATTTGTAT
AACAAACTCTTATGGTCTAATCAAGTAAATACAGTCAGTAAACAGTACTCGTTAGTTTCA
TTAGCGAAATTGAGCACACGAATCAAGAACGGACAAAACAACATAAAAGAGATTATTGAA
ATGTTTGGATCACATCTAAATATCGATTTACAACAACGTGGTGTTGAGTTTACACAACTT
TTTGGTCCATATAAACATCTAAGAGAATCACTACTCGAGAAAATGCCAGCAATGACTATT
AATAGAATAAATGGCGCAAATTCAAATGGTGAAATGATTGGTGAAGGGGAAGTGATAAGG
AGCAATAGTAGTGATAAAGTTGTGAACAATGGAAATATTCGATCAAATACAGATACATTA
CTTGATTTGCTTGGTTCTGGTGATGATATCATTTCATCATCATCATTCACTATTCCGACA
TCAACCCCGGCTCCAGCTGCAACAAACAATTTACTAGATCTTCTTGGCGATATTGACCTA
GGTGCACCAACTATATCTGTTAATAATAATAATAACAATAATAACAGTGCAACATCTCCT
ATAACAATGTCTATCCTTGACGATAACGAGAACACGAAAATTCCCGATGTTACAACAATG
TTCAACATTAATGGTAGCAGCGGTGGTAATGCTCAAGCAAATAATAGCAATTATGACCTG
GGAGATTTTCTTTCATCGCCGACTTTACACAATACTAGCGCAAAAATTATTACTGTTTTT
GATAAGAATGATTTAGTTATTACGTTTGCAACATCAAGGCACAATGATGACTATATCGAA
GTTTTGATGTCGACAACCAATAATTCAATGGATACATTAGAACAGTATTTATTTCAGGCT
GCAGTTCCTAAAAGCTTTCAATTACAAATGATGTCACCTACAGGCTCCGTCCTTTTGCCT
GGTGGTGTTATTACACAAGAAATGCGTGTTAGAAGCAATTCGCCAAGTGCCGTCCTAAGA
ATGAAATTGAGAATTTCTTTTGTGTGTAATGGAAACCCAATCTTGGAGCAAGCTGAAGTT
AGCAATTTTCCTGATGTTTAA
>g5478.t2 Gene=g5478 Length=886
MNTDSGFNPGLNMATIRQAINETIERGIMRMPTPTRLRDLIRQIRAAKTQAEERAVVNRE
CAYIRSTFREEDSVWRCRNIAKLFYIHMLGYPAHFGQLECLKLIASPKFTDKRIGYLGAM
LLLDERQDVHLLITNCLKNDLNSPTQFVVGLALCTLGAIASPEMARDLAGEIEKLMKSPN
AYIRKKAILCAFRIIRRVPELMEIFLPATRSLLNEKNHGILITGVTLITEMCENSPDTLN
HFKKIVPNLVRILKNLILAGYSPEHDVSGVSDPFLQVKILRLLRILGRNDPEASEAMNDI
LAQVATNTETSKNVGNTILYETVLTIMDIKSEGGLRVLAVNILGRFLLNNDKNIRYIALH
TLLKTVNVDISAVQRHRSTILECLKDPDVTIRKRAIELSFALVNAQNIRAMAKELLIFLE
KADPEFKAQCSSSMVLSAERYAPTIRWHLDTLLSVLIAAGNYVRDDVTSSTIQMISSSPA
NEQTYITVKFWDAIQETQDNQPLLQVAVWCIGEYGDQILYDSELEFTNERPTESTIIDLY
NKLLWSNQVNTVSKQYSLVSLAKLSTRIKNGQNNIKEIIEMFGSHLNIDLQQRGVEFTQL
FGPYKHLRESLLEKMPAMTINRINGANSNGEMIGEGEVIRSNSSDKVVNNGNIRSNTDTL
LDLLGSGDDIISSSSFTIPTSTPAPAATNNLLDLLGDIDLGAPTISVNNNNNNNNSATSP
ITMSILDDNENTKIPDVTTMFNINGSSGGNAQANNSNYDLGDFLSSPTLHNTSAKIITVF
DKNDLVITFATSRHNDDYIEVLMSTTNNSMDTLEQYLFQAAVPKSFQLQMMSPTGSVLLP
GGVITQEMRVRSNSPSAVLRMKLRISFVCNGNPILEQAEVSNFPDV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5478.t2 | Coils | Coil | Coil | 561 | 581 | - |
| 10 | g5478.t2 | Gene3D | G3DSA:1.25.10.10 | - | 19 | 619 | 2.3E-234 |
| 9 | g5478.t2 | Gene3D | G3DSA:2.60.40.1230 | - | 772 | 886 | 6.9E-30 |
| 3 | g5478.t2 | PANTHER | PTHR22780:SF29 | AP-1 COMPLEX SUBUNIT GAMMA | 25 | 745 | 0.0 |
| 5 | g5478.t2 | PANTHER | PTHR22780 | ADAPTIN, ALPHA/GAMMA/EPSILON | 25 | 745 | 0.0 |
| 4 | g5478.t2 | PANTHER | PTHR22780:SF29 | AP-1 COMPLEX SUBUNIT GAMMA | 776 | 884 | 0.0 |
| 6 | g5478.t2 | PANTHER | PTHR22780 | ADAPTIN, ALPHA/GAMMA/EPSILON | 776 | 884 | 0.0 |
| 12 | g5478.t2 | PIRSF | PIRSF037094 | AP1_gamma | 33 | 886 | 0.0 |
| 2 | g5478.t2 | Pfam | PF01602 | Adaptin N terminal region | 54 | 603 | 1.2E-131 |
| 1 | g5478.t2 | Pfam | PF02883 | Adaptin C-terminal domain | 777 | 884 | 5.3E-27 |
| 14 | g5478.t2 | ProSiteProfiles | PS50268 | Cadherins domain profile. | 630 | 737 | 8.555 |
| 15 | g5478.t2 | ProSiteProfiles | PS50180 | Gamma-adaptin ear (GAE) domain profile. | 772 | 884 | 40.581 |
| 13 | g5478.t2 | SMART | SM00809 | alpha_adaptinc2 | 770 | 884 | 6.2E-32 |
| 7 | g5478.t2 | SUPERFAMILY | SSF48371 | ARM repeat | 52 | 601 | 2.42E-97 |
| 8 | g5478.t2 | SUPERFAMILY | SSF49348 | Clathrin adaptor appendage domain | 753 | 885 | 2.44E-31 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5478/g5478.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5478.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0016192 | vesicle-mediated transport | BP |
| GO:0006886 | intracellular protein transport | BP |
| GO:0030117 | membrane coat | CC |
| GO:0005509 | calcium ion binding | MF |
| GO:0005794 | Golgi apparatus | CC |
| GO:0007156 | homophilic cell adhesion via plasma membrane adhesion molecules | BP |
| GO:0030121 | AP-1 adaptor complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12391 (AP-1 complex subunit gamma-1)
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.
