General information for g5612.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AP-1 complex subunit mu-1.
Parent gene
- The parent gene g5612 is located on chr_2: 10605463..10606853 (+ 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 | g5612 | g5612.t3 | TSS | g5612.t3 | 10603910 | 10603910 |
| chr_2 | g5612 | g5612.t3 | isoform | g5612.t3 | 10604323 | 10605463 |
| chr_2 | g5612 | g5612.t3 | exon | g5612.t3.exon1 | 10604323 | 10605463 |
| chr_2 | g5612 | g5612.t3 | cds | g5612.t3.CDS1 | 10604441 | 10605463 |
| chr_2 | g5612 | g5612.t3 | TTS | g5612.t3 | 10605558 | 10605558 |
Sequences
>g5612.t3 Gene=g5612 Length=1141
AGGAACTGTTAGTCCGCTACTTCAAACACAAGATTGCACTTTTGCTTACATCAAAACAAG
TAACTTATATATTGTAACAACTACAAGACGAAATGCAAATATTGCTTTAATTTTTACAAT
GTTACATAAAATTGTTGAAGTTTTTACTGAATATTTCAAAGAACTCGAAGAAGAATCGAT
TCGTGACAATTTTGTCATCATTTATGAGCTTCTAGATGAACTCATTGATTTTGGCTATCC
GCAGACCACAGATAGTAAAATTCTTCAAGAGTATATTACTCAGGAAGGCTATAAACTTGA
AATTCAACCGCGCATTCCAATGGCAGTTACAAATGCAGTCTCATGGCGTTCAGAAGGTAT
CAAATATCGTAAAAATGAAGTATTTTTGGATGTAATCGAAAGTGTTAATCTTTTGGCAAA
TCAAAATGGAACAGTATTGCGAAGTGAAATTGAAGGTGCAATAAAAATGAGAGTATATCT
ATCAGGCATGCCAGAACTTCGTCTGGGATTAAATGATAAAGTATTATTTGAGAGCACTGG
TCGTGGAAAATCTAAATCCATTGAGCTTGAAGATGTCAAATTTCATCAATGCGTACGATT
ATCGCGTTTTGAAAATGACAGAACGATTTCTTTTGTGCCGCCAGATGGAGAATTTGAGCT
CATGACCTACCGCAACAGTAATCAAATAAAACCTTTAATTTGGATTGAATCAGTTATTGA
AAGACACGCTCATAGTCGTATTGAGTATATGATAAAAGCTAAATCACAATTCAAACGTCG
CTCTACCGCGAATAATGTTGAAATTATCATTCCAGTACCATGTGATGCAGATTCACCTAA
ATTTAAAACAACTATTGGTAATGTGAAATATAATCCTGAACAAAATGCTATTGTATGGAA
TATCAAGAGTTTTCCAGGTGGAAAGGAATTTTTAATGCGTGCACAATTTCAATTGCCTTC
TGTTCAAAGTGAAGATGTTGAAGGAAAGCCACCAATACAAGTTCGTTTCGAAATTCCTTA
TTTTACAGTTTCTGGAATTCAAGTCAGATATTTGAAGATTATTGAAAAAAGTGGCTATCA
AGCTCTCCCTTGGGTACGATATATAACACAGAATGGTGATTATCAATTAAGAACAAATTA
A
>g5612.t3 Gene=g5612 Length=340
MLHKIVEVFTEYFKELEEESIRDNFVIIYELLDELIDFGYPQTTDSKILQEYITQEGYKL
EIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESVNLLANQNGTVLRSEIEGAIKMRVY
LSGMPELRLGLNDKVLFESTGRGKSKSIELEDVKFHQCVRLSRFENDRTISFVPPDGEFE
LMTYRNSNQIKPLIWIESVIERHAHSRIEYMIKAKSQFKRRSTANNVEIIIPVPCDADSP
KFKTTIGNVKYNPEQNAIVWNIKSFPGGKEFLMRAQFQLPSVQSEDVEGKPPIQVRFEIP
YFTVSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5612.t3 | CDD | cd09258 | AP-1_Mu1A_Cterm | 70 | 339 | 0.0 |
| 14 | g5612.t3 | Coils | Coil | Coil | 338 | 340 | - |
| 11 | g5612.t3 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 61 | 6.3E-25 |
| 12 | g5612.t3 | Gene3D | G3DSA:2.60.40.1170 | - | 81 | 334 | 1.2E-113 |
| 13 | g5612.t3 | Gene3D | G3DSA:2.60.40.1170 | - | 192 | 338 | 1.2E-113 |
| 2 | g5612.t3 | PANTHER | PTHR10529:SF257 | AP-1 COMPLEX SUBUNIT MU-1 | 2 | 339 | 2.0E-199 |
| 3 | g5612.t3 | PANTHER | PTHR10529 | AP COMPLEX SUBUNIT MU | 2 | 339 | 2.0E-199 |
| 15 | g5612.t3 | PIRSF | PIRSF005992 | AP_complex_mu | 1 | 61 | 9.4E-23 |
| 16 | g5612.t3 | PIRSF | PIRSF005992 | AP_complex_mu | 56 | 340 | 6.7E-108 |
| 5 | g5612.t3 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 18 | 45 | 1.9E-57 |
| 7 | g5612.t3 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 76 | 104 | 1.9E-57 |
| 8 | g5612.t3 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 150 | 177 | 1.9E-57 |
| 6 | g5612.t3 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 219 | 234 | 1.9E-57 |
| 4 | g5612.t3 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 259 | 270 | 1.9E-57 |
| 1 | g5612.t3 | Pfam | PF00928 | Adaptor complexes medium subunit family | 74 | 338 | 1.4E-93 |
| 18 | g5612.t3 | ProSitePatterns | PS00990 | Clathrin adaptor complexes medium chain signature 1. | 74 | 94 | - |
| 19 | g5612.t3 | ProSiteProfiles | PS51072 | Mu homology domain (MHD) profile. | 85 | 338 | 47.046 |
| 9 | g5612.t3 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 58 | 2.15E-19 |
| 10 | g5612.t3 | SUPERFAMILY | SSF49447 | Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 74 | 338 | 5.89E-101 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5612/g5612.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5612.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006886 | intracellular protein transport | BP |
| GO:0030131 | clathrin adaptor complex | 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.
