General information for g15819.t2
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 g15819 is located on chr_4: 6874219..6876786 (+ 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_4 | g15819 | g15819.t2 | TSS | g15819.t2 | 6873691 | 6873691 |
| chr_4 | g15819 | g15819.t2 | isoform | g15819.t2 | 6873803 | 6876786 |
| chr_4 | g15819 | g15819.t2 | exon | g15819.t2.exon1 | 6873803 | 6873920 |
| chr_4 | g15819 | g15819.t2 | cds | g15819.t2.CDS1 | 6873803 | 6873920 |
| chr_4 | g15819 | g15819.t2 | exon | g15819.t2.exon2 | 6874219 | 6874859 |
| chr_4 | g15819 | g15819.t2 | cds | g15819.t2.CDS2 | 6874219 | 6874859 |
| chr_4 | g15819 | g15819.t2 | exon | g15819.t2.exon3 | 6874917 | 6875190 |
| chr_4 | g15819 | g15819.t2 | cds | g15819.t2.CDS3 | 6874917 | 6875190 |
| chr_4 | g15819 | g15819.t2 | exon | g15819.t2.exon4 | 6875431 | 6876786 |
| chr_4 | g15819 | g15819.t2 | cds | g15819.t2.CDS4 | 6875431 | 6875654 |
| chr_4 | g15819 | g15819.t2 | TTS | g15819.t2 | NA | NA |
Sequences
>g15819.t2 Gene=g15819 Length=2389
ATGATCTTTCAAATTTTTCTCCTCGATGTCAAAGGAAAAGTTTTGGTATCGAGAAATTAT
CGAGGTGAAATTGATTCATCAGTGATTGATAAATTTATGCCAATGCTCATGGAAAAAGGA
ATAGTAACACCAATAATTCAAACTGCCGAATGTACATTCGCCTATATAAAAACCAATAAT
CTCTACATTGTATCAACAACAAAAAAGAATGCAAATATTGCACTTGTTTTTACAATGCTT
CATAAAATTGTTCAAGTTTTTACTGAATATTTTAAAGAACTTGAAGAAGAATCAATTCGT
GATAATTTTGTAATAATTTATGAACTTCTTGATGAACTTATTGATTTTGGTTATCCACAA
ACAACAGATAGTAAAATTTTACAAGAATACATCACACAAGAAGGACATAAACTTGAAATT
CAACCTCGAATTCCAATGGCTGTCACAAATGCCGTTTCATGGCGTTCAGAAGGAATAAAA
TATCGTAAAAATGAAGTTTTTTTGGATGTCATTGAAAGTGTAAACCTTTTGGCAAATGCA
AATGGAAATGTTTTACGTAGTGAAATTGTTGGTGCAATAAAAATGCGAGTTTATCTTTCG
GGCATGCCAGAATTACGTCTTGGTCTCAATGACAAAGTCCTTTTTGAGTCAACTGGTCGT
GGCAAGTCAAAATCAATTGAACTTGAAGATGTCAAATTTCATCAATGTGTTCGACTTTCA
CGATTTGAAAATGACAGGACAATTTCTTTTATACCACCGGATGGTGAATTTGAGCTCATG
ACCTACCGTAATAGTGCACATATGAAACCACTTATTTGGATTGAATCTGTGATTGAAAGA
CATGCACATAGTCGAGTTGAGTACATGATCAAGGCAAAATCACAATTTAAAAGGCGTTCG
ACAGCAAACAATGTCGAAATTATTATTCCTGTACCAAATGATGCTGACAGTCCTAAATTT
AAAACTACTATTGGAAGTGTGAAATATACACCAGAACAGAGTGCTGTTACGTGGAGTATT
AAATCTTTTCCTGGTGGAAAAGAATTTCTAATGCGAGCACATTTTGGTCTACCATCAGTT
GAATGTGAAGACAGCGAAGGAAAGCCACCAATTCAAGTTAAATTTGAGATTCCTTATTTT
ACAACATCTGGAATTCAAGTAAGATATTTAAAAATTATTGAAAAAAGTGGATATCAGGCA
TTACCTTGGGTTAGATATATTACACAAAATGGTGATTATCAATTGCGAACTAATTAAAAT
AGAATTTAGGATTTTTATATATTTCATATTTATTTTTTGATATATTCATAATTTACAATC
TAGTTTTACAAAAAAATAAAATTTAGTTCATTTATTATCTATTATTTTATTTACCTTTCA
AAATGAATGACAAATTTTGACCTTAAGAAGGTCATGTTGAAAATTTGACTTTTGTGATGA
TAAATTAAATTTTTTGGAAAATTAACTAAAATTTCGATCAACATATGAAAACTTTCTGAT
TTTGTATTAATTTGTTTAAAAAAATTAAAAACTTAACCTAAGAACTTTTGACATTGCTAA
AACAAAAAATGATATACACTATTAGTGTTTAGTCAAGTTCAAAATTTTTAAAATATTCAA
TTTGGATTTACACTAACTGCCAATAAATTTTAGATAAAATGGACTACAGTCTTCTCTCGG
ATATAAGGAATAGTTCTTGTATTCGAATCAAAACATGACATATTTAACAATGTAAAAATT
TTTAAAAACTGTTAAATTTTTTTAAAAAAAAATCTGGTAAATTTTTAAACTTACAAAGAA
AATCATTATTTTTTAACGGTTTTTTCAAATGCGTTTCTTGTATTCAAATTTCTTTCTATA
CAAAACAAAAACCAAATTTTCGGAAAAATTTTCAATCAAATTCAAAAATTTTATTTCCGA
GGGAAGAATTTTAATGTTTTATTGACATTTCTGAAAACAACTCAAAATAATTTGAACCGA
AATGTATGTCAAAGTTCTGTTTAAAATTTTCTATAGAAATTCATCTTTGATTATTTGAGT
AATAAATTTTCCAATAATCTTCAACTTTTATGTTCAAAAAATTGTCTAAAAATTTAAAGT
GTTGATTAAATATAAAACTTAAAACATTGAAAAGACTCAATCAAGACAAGAATTTAAAAC
TTGAATAAATTTTTTTAATGAAATTAAAAATTTCAAGTGCTAAAATTATAAACGAAATAA
ATTTTGTACAAAATGACAAGTAGTTATTAGAGTAAGAAACTATTTAATCATTTCAATTAA
TATTTATTACCATAATTATTAATTATTTTTGCACATAAAATTATTTTGCTTAACACTTAT
AAAATTATTTTTATGTAAACAAAAATAAATAAAATATTTGTTTTAAAAT
>g15819.t2 Gene=g15819 Length=418
MIFQIFLLDVKGKVLVSRNYRGEIDSSVIDKFMPMLMEKGIVTPIIQTAECTFAYIKTNN
LYIVSTTKKNANIALVFTMLHKIVQVFTEYFKELEEESIRDNFVIIYELLDELIDFGYPQ
TTDSKILQEYITQEGHKLEIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESVNLLANA
NGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKSKSIELEDVKFHQCVRLS
RFENDRTISFIPPDGEFELMTYRNSAHMKPLIWIESVIERHAHSRVEYMIKAKSQFKRRS
TANNVEIIIPVPNDADSPKFKTTIGSVKYTPEQSAVTWSIKSFPGGKEFLMRAHFGLPSV
ECEDSEGKPPIQVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g15819.t2 | CDD | cd14835 | AP1_Mu_N | 5 | 138 | 3.52163E-84 |
| 18 | g15819.t2 | CDD | cd09258 | AP-1_Mu1A_Cterm | 148 | 417 | 0.0 |
| 13 | g15819.t2 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 139 | 1.1E-50 |
| 15 | g15819.t2 | Gene3D | G3DSA:2.60.40.1170 | - | 159 | 412 | 1.8E-112 |
| 14 | g15819.t2 | Gene3D | G3DSA:2.60.40.1170 | - | 270 | 416 | 1.8E-112 |
| 3 | g15819.t2 | PANTHER | PTHR10529:SF257 | AP-1 COMPLEX SUBUNIT MU-1 | 5 | 417 | 4.8E-237 |
| 4 | g15819.t2 | PANTHER | PTHR10529 | AP COMPLEX SUBUNIT MU | 5 | 417 | 4.8E-237 |
| 16 | g15819.t2 | PIRSF | PIRSF005992 | AP_complex_mu | 1 | 418 | 8.7E-143 |
| 8 | g15819.t2 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 12 | 32 | 1.1E-67 |
| 7 | g15819.t2 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 96 | 123 | 1.1E-67 |
| 5 | g15819.t2 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 154 | 182 | 1.1E-67 |
| 9 | g15819.t2 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 228 | 255 | 1.1E-67 |
| 6 | g15819.t2 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 297 | 312 | 1.1E-67 |
| 10 | g15819.t2 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 337 | 348 | 1.1E-67 |
| 2 | g15819.t2 | Pfam | PF01217 | Clathrin adaptor complex small chain | 1 | 129 | 1.9E-7 |
| 1 | g15819.t2 | Pfam | PF00928 | Adaptor complexes medium subunit family | 152 | 416 | 1.4E-90 |
| 20 | g15819.t2 | ProSitePatterns | PS00990 | Clathrin adaptor complexes medium chain signature 1. | 152 | 172 | - |
| 19 | g15819.t2 | ProSitePatterns | PS00991 | Clathrin adaptor complexes medium chain signature 2. | 248 | 262 | - |
| 21 | g15819.t2 | ProSiteProfiles | PS51072 | Mu homology domain (MHD) profile. | 163 | 416 | 46.706 |
| 11 | g15819.t2 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 136 | 2.29E-40 |
| 12 | g15819.t2 | SUPERFAMILY | SSF49447 | Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 152 | 416 | 4.45E-100 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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 transcript has been annotated with K12393 (AP-1 complex subunit mu)
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.
