General information for g5478.t1
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.t1 | TTS | g5478.t1 | 9805274 | 9805274 |
| chr_2 | g5478 | g5478.t1 | isoform | g5478.t1 | 9805787 | 9810267 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon1 | 9805787 | 9805879 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS1 | 9805787 | 9805879 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon2 | 9805939 | 9806049 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS2 | 9805939 | 9806049 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon3 | 9806112 | 9806850 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS3 | 9806112 | 9806850 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon4 | 9806912 | 9807053 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS4 | 9806912 | 9807053 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon5 | 9807123 | 9807543 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS5 | 9807123 | 9807543 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon6 | 9807608 | 9808030 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS6 | 9807608 | 9808030 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon7 | 9808725 | 9808801 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS7 | 9808725 | 9808801 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon8 | 9808862 | 9809100 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS8 | 9808862 | 9809100 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon9 | 9809166 | 9809496 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS9 | 9809166 | 9809496 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon10 | 9809634 | 9809695 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS10 | 9809634 | 9809695 |
| chr_2 | g5478 | g5478.t1 | exon | g5478.t1.exon11 | 9810251 | 9810267 |
| chr_2 | g5478 | g5478.t1 | cds | g5478.t1.CDS11 | 9810251 | 9810267 |
| chr_2 | g5478 | g5478.t1 | TSS | g5478.t1 | 9811058 | 9811058 |
Sequences
>g5478.t1 Gene=g5478 Length=2655
ATGAATACAGATAGCGGATTTAATCCTGGCTTAAACATGGCCACAATTCGTCAAGCGATA
AATGAGACAATTGAAAGGGTGCGTATGCCTACACCAACGAGACTTAGAGATCTGATTCGT
CAAATTCGTGCTGCAAAAACACAAGCAGAAGAACGAGCTGTTGTAAATCGAGAATGTGCC
TATATTCGATCGACATTCAGAGAAGAAGATTCCGTTTGGCGATGCAGGAATATAGCAAAA
CTTTTTTACATTCATATGCTAGGATATCCAGCACACTTTGGACAACTTGAGTGTCTAAAA
CTAATTGCAAGTCCTAAATTTACTGATAAGCGTATTGGATATTTAGGTGCAATGCTTTTA
CTGGATGAGCGTCAAGATGTTCATTTGCTCATAACAAACTGCTTAAAAAATGACCTTAAT
AGTCCAACACAATTTGTTGTTGGTTTAGCGCTTTGTACTCTTGGTGCAATTGCATCTCCT
GAAATGGCGAGGGATTTAGCAGGAGAAATTGAGAAATTAATGAAGTCACCAAATGCGTAT
ATTCGAAAAAAGGCCATTCTTTGCGCTTTCAGAATAATTCGTCGTGTGCCTGAACTAATG
GAAATATTTCTACCTGCTACACGATCGTTGTTAAATGAGAAAAATCATGGGATACTCATA
ACTGGTGTTACGCTAATCACTGAAATGTGTGAAAATAGTCCAGACACATTAAATCATTTT
AAAAAGATTGTTCCAAATTTAGTACGCATTTTGAAAAATCTAATTCTTGCTGGTTATTCT
CCCGAACACGATGTAAGTGGAGTATCTGATCCATTTTTACAAGTAAAAATTTTACGATTG
TTGAGAATTCTTGGGCGAAATGATCCTGAAGCATCGGAAGCGATGAATGACATTCTTGCA
CAAGTTGCAACAAATACTGAAACAAGTAAAAATGTTGGAAATACGATCTTATATGAAACT
GTTCTTACTATAATGGATATAAAATCAGAGGGTGGATTACGAGTGCTCGCAGTTAATATA
CTTGGAAGATTTTTATTAAATAATGATAAAAATATTCGTTACATAGCATTGCATACACTG
TTAAAAACAGTAAATGTAGATATATCTGCAGTTCAACGCCATCGTAGTACGATTCTCGAA
TGTTTGAAGGATCCTGATGTTACTATTCGAAAACGAGCAATCGAGTTATCATTTGCATTA
GTAAATGCTCAAAATATAAGAGCAATGGCTAAAGAATTGTTGATATTTTTAGAAAAAGCA
GATCCTGAATTTAAAGCTCAGTGTAGTTCAAGCATGGTATTGTCAGCAGAACGATATGCT
CCAACTATACGTTGGCATTTAGATACACTTTTAAGTGTTCTTATAGCAGCAGGAAATTAT
GTACGTGATGATGTCACTTCATCTACTATTCAAATGATTTCTAGTAGTCCAGCAAACGAA
CAGACGTACATTACTGTAAAATTTTGGGATGCAATTCAAGAAACACAAGACAATCAACCT
CTTTTACAAGTAGCCGTGTGGTGTATTGGAGAATATGGGGATCAAATTCTTTACGATTCT
GAATTGGAATTTACAAATGAAAGACCTACGGAATCAACAATTATTGATTTGTATAACAAA
CTCTTATGGTCTAATCAAGTAAATACAGTCAGTAAACAGTACTCGTTAGTTTCATTAGCG
AAATTGAGCACACGAATCAAGAACGGACAAAACAACATAAAAGAGATTATTGAAATGTTT
GGATCACATCTAAATATCGATTTACAACAACGTGGTGTTGAGTTTACACAACTTTTTGGT
CCATATAAACATCTAAGAGAATCACTACTCGAGAAAATGCCAGCAATGACTATTAATAGA
ATAAATGGCGCAAATTCAAATGGTGAAATGATTGGTGAAGGGGAAGTGATAAGGAGCAAT
AGTAGTGATAAAGTTGTGAACAATGGAAATATTCGATCAAATACAGATACATTACTTGAT
TTGCTTGGTTCTGGTGATGATATCATTTCATCATCATCATTCACTATTCCGACATCAACC
CCGGCTCCAGCTGCAACAAACAATTTACTAGATCTTCTTGGCGATATTGACCTAGGTGCA
CCAACTATATCTGTTAATAATAATAATAACAATAATAACAGTGCAACATCTCCTATAACA
ATGTCTATCCTTGACGATAACGAGAACACGAAAATTCCCGATGTTACAACAATGTTCAAC
ATTAATGGTAGCAGCGGTGGTAATGCTCAAGCAAATAATAGCAATTATGACCTGGGAGAT
TTTCTTTCATCGCCGACTTTACACAATACTAGCGCAAAAATTATTACTGTTTTTGATAAG
AATGATTTAGTTATTACGTTTGCAACATCAAGGCACAATGATGACTATATCGAAGTTTTG
ATGTCGACAACCAATAATTCAATGGATACATTAGAACAGTATTTATTTCAGGCTGCAGTT
CCTAAAAGCTTTCAATTACAAATGATGTCACCTACAGGCTCCGTCCTTTTGCCTGGTGGT
GTTATTACACAAGAAATGCGTGTTAGAAGCAATTCGCCAAGTGCCGTCCTAAGAATGAAA
TTGAGAATTTCTTTTGTGTGTAATGGAAACCCAATCTTGGAGCAAGCTGAAGTTAGCAAT
TTTCCTGATGTTTAA
>g5478.t1 Gene=g5478 Length=884
MNTDSGFNPGLNMATIRQAINETIERVRMPTPTRLRDLIRQIRAAKTQAEERAVVNRECA
YIRSTFREEDSVWRCRNIAKLFYIHMLGYPAHFGQLECLKLIASPKFTDKRIGYLGAMLL
LDERQDVHLLITNCLKNDLNSPTQFVVGLALCTLGAIASPEMARDLAGEIEKLMKSPNAY
IRKKAILCAFRIIRRVPELMEIFLPATRSLLNEKNHGILITGVTLITEMCENSPDTLNHF
KKIVPNLVRILKNLILAGYSPEHDVSGVSDPFLQVKILRLLRILGRNDPEASEAMNDILA
QVATNTETSKNVGNTILYETVLTIMDIKSEGGLRVLAVNILGRFLLNNDKNIRYIALHTL
LKTVNVDISAVQRHRSTILECLKDPDVTIRKRAIELSFALVNAQNIRAMAKELLIFLEKA
DPEFKAQCSSSMVLSAERYAPTIRWHLDTLLSVLIAAGNYVRDDVTSSTIQMISSSPANE
QTYITVKFWDAIQETQDNQPLLQVAVWCIGEYGDQILYDSELEFTNERPTESTIIDLYNK
LLWSNQVNTVSKQYSLVSLAKLSTRIKNGQNNIKEIIEMFGSHLNIDLQQRGVEFTQLFG
PYKHLRESLLEKMPAMTINRINGANSNGEMIGEGEVIRSNSSDKVVNNGNIRSNTDTLLD
LLGSGDDIISSSSFTIPTSTPAPAATNNLLDLLGDIDLGAPTISVNNNNNNNNSATSPIT
MSILDDNENTKIPDVTTMFNINGSSGGNAQANNSNYDLGDFLSSPTLHNTSAKIITVFDK
NDLVITFATSRHNDDYIEVLMSTTNNSMDTLEQYLFQAAVPKSFQLQMMSPTGSVLLPGG
VITQEMRVRSNSPSAVLRMKLRISFVCNGNPILEQAEVSNFPDV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5478.t1 | Coils | Coil | Coil | 559 | 579 | - |
| 10 | g5478.t1 | Gene3D | G3DSA:1.25.10.10 | - | 18 | 617 | 4.0E-234 |
| 9 | g5478.t1 | Gene3D | G3DSA:2.60.40.1230 | - | 770 | 884 | 6.8E-30 |
| 3 | g5478.t1 | PANTHER | PTHR22780:SF29 | AP-1 COMPLEX SUBUNIT GAMMA | 24 | 743 | 0.0 |
| 5 | g5478.t1 | PANTHER | PTHR22780 | ADAPTIN, ALPHA/GAMMA/EPSILON | 24 | 743 | 0.0 |
| 4 | g5478.t1 | PANTHER | PTHR22780:SF29 | AP-1 COMPLEX SUBUNIT GAMMA | 774 | 882 | 0.0 |
| 6 | g5478.t1 | PANTHER | PTHR22780 | ADAPTIN, ALPHA/GAMMA/EPSILON | 774 | 882 | 0.0 |
| 12 | g5478.t1 | PIRSF | PIRSF037094 | AP1_gamma | 31 | 884 | 0.0 |
| 2 | g5478.t1 | Pfam | PF01602 | Adaptin N terminal region | 52 | 601 | 1.2E-131 |
| 1 | g5478.t1 | Pfam | PF02883 | Adaptin C-terminal domain | 775 | 882 | 5.3E-27 |
| 14 | g5478.t1 | ProSiteProfiles | PS50268 | Cadherins domain profile. | 628 | 735 | 8.555 |
| 15 | g5478.t1 | ProSiteProfiles | PS50180 | Gamma-adaptin ear (GAE) domain profile. | 770 | 882 | 40.581 |
| 13 | g5478.t1 | SMART | SM00809 | alpha_adaptinc2 | 768 | 882 | 6.2E-32 |
| 7 | g5478.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 50 | 599 | 2.42E-97 |
| 8 | g5478.t1 | SUPERFAMILY | SSF49348 | Clathrin adaptor appendage domain | 751 | 883 | 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.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5478.t1.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.
