General information for g5478.t5
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.t5 | isoform | g5478.t5 | 9808875 | 9811064 |
| chr_2 | g5478 | g5478.t5 | exon | g5478.t5.exon1 | 9808875 | 9809100 |
| chr_2 | g5478 | g5478.t5 | cds | g5478.t5.CDS1 | 9808875 | 9809100 |
| chr_2 | g5478 | g5478.t5 | exon | g5478.t5.exon2 | 9809166 | 9809496 |
| chr_2 | g5478 | g5478.t5 | cds | g5478.t5.CDS2 | 9809166 | 9809496 |
| chr_2 | g5478 | g5478.t5 | exon | g5478.t5.exon3 | 9809634 | 9809695 |
| chr_2 | g5478 | g5478.t5 | cds | g5478.t5.CDS3 | 9809634 | 9809695 |
| chr_2 | g5478 | g5478.t5 | exon | g5478.t5.exon4 | 9810251 | 9811064 |
| chr_2 | g5478 | g5478.t5 | cds | g5478.t5.CDS4 | 9810251 | 9810267 |
| chr_2 | g5478 | g5478.t5 | TSS | g5478.t5 | 9811058 | 9811058 |
| chr_2 | g5478 | g5478.t5 | TTS | g5478.t5 | NA | NA |
Sequences
>g5478.t5 Gene=g5478 Length=1433
AAAGCTTTTGCTCAACCAGAAGAGAAAATTAAATTCATAAAAATCAAGAAAAATTGCAAA
ATTGCAAAGAAATATTAGTGATTACTTCAATTTTATTTCATAAATCGGTATACTATAACC
GCTGGTCTGCAATAGTATATTTTAAACTTGTTTTTTACCCCAAAAAGTGTGCGAAATATA
AAATCTTAATTTTTCGCTAAATGTCTTATTAATATCATCATCATCATTTTGAAAAAAAAT
TACAAAGTGTTATCGTGTTATCAATCAAAATCTTTTACGTTTGTATTTAATAAATAATGC
GCATAAAAAGAATATAATAATGCTAGAAAATATCATTATGTGTTCGAAGTGATAAAGAAA
AAAACTTGAGCAATATTTGAGTGAAGGAAATTGGACTTGAAAATTTTCAAAGTCACATCC
AATCTGTGCATAAGCACTTTATAAAAACTATTTCGATTAAACTTATAAATTGTTTTTAAA
TACATCGATGAATCATAAAAATTCCAAATATTAAAGTTGTTTTATAACCTGCGAATTAAA
AATATTGGACAAAAAAGAACTGCGGACGTGTGTGACACTGTTGTTGTTGTTAACTCAGTT
AATTGAAAAATATTTTCCTCGTTGTCGCCTTACTGTGACATTCCGTTCTCACTCCACCCA
TAAATCTACATACCTAGTTTTTACCTTTGTGTTTTGTTTTCCTTACTATCCTTTTTTGTT
AAAAAAGTGGTGCTTCATTTTATTATAAAGAGTGTAATATTCAAATCGTGTTTAAGTAAC
ATATATAACAAACCATCATGAATACAGATAGCGGATTTAATCCTGGCTTAAACATGGCCA
CAATTCGTCAAGCGATAAATGAGACAATTGAAAGGGTGCGTATGCCTACACCAACGAGAC
TTAGAGATCTGATTCGTCAAATTCGTGCTGCAAAAACACAAGCAGAAGAACGAGCTGTTG
TAAATCGAGAATGTGCCTATATTCGATCGACATTCAGAGAAGAAGATTCCGTTTGGCGAT
GCAGGAATATAGCAAAACTTTTTTACATTCATATGCTAGGATATCCAGCACACTTTGGAC
AACTTGAGTGTCTAAAACTAATTGCAAGTCCTAAATTTACTGATAAGCGTATTGGATATT
TAGGTGCAATGCTTTTACTGGATGAGCGTCAAGATGTTCATTTGCTCATAACAAACTGCT
TAAAAAATGACCTTAATAGTCCAACACAATTTGTTGTTGGTTTAGCGCTTTGTACTCTTG
GTGCAATTGCATCTCCTGAAATGGCGAGGGATTTAGCAGGAGAAATTGAGAAATTAATGA
AGTCACCAAATGCGTATATTCGAAAAAAGGCCATTCTTTGCGCTTTCAGAATAATTCGTC
GTGTGCCTGAACTAATGGAAATATTTCTACCTGCTACACGATCGTTGTTAAAT
>g5478.t5 Gene=g5478 Length=212
MNTDSGFNPGLNMATIRQAINETIERVRMPTPTRLRDLIRQIRAAKTQAEERAVVNRECA
YIRSTFREEDSVWRCRNIAKLFYIHMLGYPAHFGQLECLKLIASPKFTDKRIGYLGAMLL
LDERQDVHLLITNCLKNDLNSPTQFVVGLALCTLGAIASPEMARDLAGEIEKLMKSPNAY
IRKKAILCAFRIIRRVPELMEIFLPATRSLLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5478.t5 | Gene3D | G3DSA:1.25.10.10 | - | 17 | 212 | 0 |
| 2 | g5478.t5 | PANTHER | PTHR22780:SF29 | AP-1 COMPLEX SUBUNIT GAMMA | 24 | 211 | 0 |
| 3 | g5478.t5 | PANTHER | PTHR22780 | ADAPTIN, ALPHA/GAMMA/EPSILON | 24 | 211 | 0 |
| 1 | g5478.t5 | Pfam | PF01602 | Adaptin N terminal region | 52 | 212 | 0 |
| 4 | g5478.t5 | SUPERFAMILY | SSF48371 | ARM repeat | 50 | 212 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5478/g5478.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5478.t5.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.
