General information for g5478.t4
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.t4 | isoform | g5478.t4 | 9808725 | 9811398 |
| chr_2 | g5478 | g5478.t4 | exon | g5478.t4.exon1 | 9808725 | 9808801 |
| chr_2 | g5478 | g5478.t4 | cds | g5478.t4.CDS1 | 9808725 | 9808801 |
| chr_2 | g5478 | g5478.t4 | exon | g5478.t4.exon2 | 9808862 | 9809100 |
| chr_2 | g5478 | g5478.t4 | cds | g5478.t4.CDS2 | 9808862 | 9809100 |
| chr_2 | g5478 | g5478.t4 | exon | g5478.t4.exon3 | 9809166 | 9809496 |
| chr_2 | g5478 | g5478.t4 | cds | g5478.t4.CDS3 | 9809166 | 9809496 |
| chr_2 | g5478 | g5478.t4 | exon | g5478.t4.exon4 | 9809634 | 9809695 |
| chr_2 | g5478 | g5478.t4 | cds | g5478.t4.CDS4 | 9809634 | 9809695 |
| chr_2 | g5478 | g5478.t4 | exon | g5478.t4.exon5 | 9810251 | 9811398 |
| chr_2 | g5478 | g5478.t4 | cds | g5478.t4.CDS5 | 9810251 | 9810267 |
| chr_2 | g5478 | g5478.t4 | TSS | g5478.t4 | 9811538 | 9811538 |
| chr_2 | g5478 | g5478.t4 | TTS | g5478.t4 | NA | NA |
Sequences
>g5478.t4 Gene=g5478 Length=1857
GGTAATTTAAAATTGCAATGCGATGCAATTTACATTTTCTTTAGAACTGATAATTGAATT
TATTTCATGAACTCATAATTATGGTAAACATTTTCATATCTGATTCTTTGTTCGTTTAAT
GTTAAACTGATCCTTAATCAAAAACAAAAGAAAAATTAATATCATTGTTTAGTCATCTTT
AATTGTAACATAGGAATCAATCAAAAGTGATTTTTAAGAACTCTACATTCTACAAAAATC
TCATTTCATAATAATTTGACAAAACAGTATTCGCCGTTAAAAAAAGTGCGCCGCTGAATT
TTCAAGTTAACAGAGAATTGTAGTTTATTAGAAAAAAGCTTTTGCTCAACCAGAAGAGAA
AATTAAATTCATAAAAATCAAGAAAAATTGCAAAATTGCAAAGAAATATTAGTGATTACT
TCAATTTTATTTCATAAATCGGTATACTATAACCGCTGGTCTGCAATAGTATATTTTAAA
CTTGTTTTTTACCCCAAAAAGTGTGCGAAATATAAAATCTTAATTTTTCGCTAAATGTCT
TATTAATATCATCATCATCATTTTGAAAAAAAATTACAAAGTGTTATCGTGTTATCAATC
AAAATCTTTTACGTTTGTATTTAATAAATAATGCGCATAAAAAGAATATAATAATGCTAG
AAAATATCATTATGTGTTCGAAGTGATAAAGAAAAAAACTTGAGCAATATTTGAGTGAAG
GAAATTGGACTTGAAAATTTTCAAAGTCACATCCAATCTGTGCATAAGCACTTTATAAAA
ACTATTTCGATTAAACTTATAAATTGTTTTTAAATACATCGATGAATCATAAAAATTCCA
AATATTAAAGTTGTTTTATAACCTGCGAATTAAAAATATTGGACAAAAAAGAACTGCGGA
CGTGTGTGACACTGTTGTTGTTGTTAACTCAGTTAATTGAAAAATATTTTCCTCGTTGTC
GCCTTACTGTGACATTCCGTTCTCACTCCACCCATAAATCTACATACCTAGTTTTTACCT
TTGTGTTTTGTTTTCCTTACTATCCTTTTTTGTTAAAAAAGTGGTGCTTCATTTTATTAT
AAAGAGTGTAATATTCAAATCGTGTTTAAGTAACATATATAACAAACCATCATGAATACA
GATAGCGGATTTAATCCTGGCTTAAACATGGCCACAATTCGTCAAGCGATAAATGAGACA
ATTGAAAGGGTGCGTATGCCTACACCAACGAGACTTAGAGATCTGATTCGTCAAATTCGT
GCTGCAAAAACACAAGCAGAAGAACGAGCTGTTGTAAATCGAGAATGTGCCTATATTCGA
TCGACATTCAGAGAAGAAGATTCCGTTTGGCGATGCAGGAATATAGCAAAACTTTTTTAC
ATTCATATGCTAGGATATCCAGCACACTTTGGACAACTTGAGTGTCTAAAACTAATTGCA
AGTCCTAAATTTACTGATAAGCGTATTGGATATTTAGGTGCAATGCTTTTACTGGATGAG
CGTCAAGATGTTCATTTGCTCATAACAAACTGCTTAAAAAATGACCTTAATAGTCCAACA
CAATTTGTTGTTGGTTTAGCGCTTTGTACTCTTGGTGCAATTGCATCTCCTGAAATGGCG
AGGGATTTAGCAGGAGAAATTGAGAAATTAATGAAGTCACCAAATGCGTATATTCGAAAA
AAGGCCATTCTTTGCGCTTTCAGAATAATTCGTCGTGTGCCTGAACTAATGGAAATATTT
CTACCTGCTACACGATCGTTGTTAAATGAGAAAAATCATGGGATACTCATAACTGGTGTT
ACGCTAATCACTGAAATGTGTGAAAATAGTCCAGACACATTAAATCATTTTAAAAAG
>g5478.t4 Gene=g5478 Length=242
MNTDSGFNPGLNMATIRQAINETIERVRMPTPTRLRDLIRQIRAAKTQAEERAVVNRECA
YIRSTFREEDSVWRCRNIAKLFYIHMLGYPAHFGQLECLKLIASPKFTDKRIGYLGAMLL
LDERQDVHLLITNCLKNDLNSPTQFVVGLALCTLGAIASPEMARDLAGEIEKLMKSPNAY
IRKKAILCAFRIIRRVPELMEIFLPATRSLLNEKNHGILITGVTLITEMCENSPDTLNHF
KK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5478.t4 | Gene3D | G3DSA:1.25.10.10 | - | 17 | 242 | 0 |
| 2 | g5478.t4 | PANTHER | PTHR22780:SF29 | AP-1 COMPLEX SUBUNIT GAMMA | 24 | 238 | 0 |
| 3 | g5478.t4 | PANTHER | PTHR22780 | ADAPTIN, ALPHA/GAMMA/EPSILON | 24 | 238 | 0 |
| 1 | g5478.t4 | Pfam | PF01602 | Adaptin N terminal region | 52 | 235 | 0 |
| 4 | g5478.t4 | SUPERFAMILY | SSF48371 | ARM repeat | 50 | 236 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5478/g5478.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5478.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006886 | intracellular protein transport | BP |
| GO:0030117 | membrane coat | CC |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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. There were no conditions that were differentially expressed