General information for g14458.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AP-3 complex subunit mu-1.
Parent gene
- The parent gene g14458 is located on chr_4: 683999..685218 (+ 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 | g14458 | g14458.t4 | TSS | g14458.t4 | 683697 | 683697 |
| chr_4 | g14458 | g14458.t4 | isoform | g14458.t4 | 683767 | 685218 |
| chr_4 | g14458 | g14458.t4 | exon | g14458.t4.exon1 | 683767 | 683883 |
| chr_4 | g14458 | g14458.t4 | cds | g14458.t4.CDS1 | 683767 | 683883 |
| chr_4 | g14458 | g14458.t4 | exon | g14458.t4.exon2 | 683976 | 684687 |
| chr_4 | g14458 | g14458.t4 | cds | g14458.t4.CDS2 | 683976 | 684687 |
| chr_4 | g14458 | g14458.t4 | exon | g14458.t4.exon3 | 684760 | 685113 |
| chr_4 | g14458 | g14458.t4 | cds | g14458.t4.CDS3 | 684760 | 685113 |
| chr_4 | g14458 | g14458.t4 | exon | g14458.t4.exon4 | 685172 | 685218 |
| chr_4 | g14458 | g14458.t4 | cds | g14458.t4.CDS4 | 685172 | 685218 |
| chr_4 | g14458 | g14458.t4 | TTS | g14458.t4 | 685374 | 685374 |
Sequences
>g14458.t4 Gene=g14458 Length=1230
ATGGAAAGTCTTTTTATTATTAATTCATCTGGTGATGTTTTTCTTGAGAAACATTGGAGA
AGTGTTATATCAAAGGGAATTTGTGATTATTTCTTGGAAAGATTGAAAAATTCTAATGAC
GTTGTACCAATCATTCCGACATCAATGAACTCAACAAATCTCGTCTCAATTAACCGTTGT
GGTGTTTATTTTGTTACTGTCTGTAAATCAGAAATTTCGCCACTTTTTGTGATTGAATTT
TTGCATCGAGTTGTTGATATTTTTGTTGATTATTTCAATGAATGCAATGAGACTGTAATT
AAAGAAAATTATGTAGTTATTTATGAATTACTTGATGAAATGCTTGATAACGGATTCCCT
TTGGCAACAGAATCTAACGTTTTAAAAGAACTTATTAAACCTCCAAATGTTTTTCGGACA
ATTGCAAATTCAGTAACTGGAAAAACTAATTTCAGTGACACTTTGCCTGTCGGTTCACTC
TCAGCAATTCCGTGGCGAAAGTCTGGTGTCAAATATACAAATAATGAAGCATATTTTGAT
GTTATTGAAGAAGTTGATGCAATTATTGACAAATCTGGTTCGACAATTTTTGCTGAAATT
TCTGGTGAAATCCAGTGTTTGATTAAACTTAGCGGCATGCCTGATCTTTCATTATCATTT
GTCAATCCACGAATTCTCGATGACGTTTCATTCCATCCATGTGTTAGATTTAAGCGATGG
GAAACTGAAAGAGTTTTGAGCTTCATTCCACCTGATGGCGGTTTTCGGTTGATGTCGTAT
CATGTTACATCACAAAGTGTTCCGATTCCAATTTATTTAAGACATGTTAGCGAACAAGGT
CGACTTGACATCACTGTTGGTCCAAAAACAACACTTGGTCGAACACTTGAGAGTGTAAAA
CTTGAAATTTTGTTCCCCAAAAGTGTCGTGAATTGCAGTCTCGTGACCACTCAAGGAAAA
TATGTTTTTGATCAAAATTCAAAAATTCTTAATTGGGATGTTGGCAAAATTGATGTTCAA
AAGTTGCCGAATATTAGAGGAAGTGTAACAGTTATGGCAGGAACAACTATTGAATCAATG
CCATCAATTAATGTGCAATTTACAATCTCACAATTGGCAGTTTCGGGATTGAAAGTTAAT
CGATTAGATATGTACGGAGATGTAAAATACAAACCTTTCAAAGGTGTTAAATATGTAACC
AAGGCAGGAAAATTCCAAATTCGTCTTTAA
>g14458.t4 Gene=g14458 Length=409
MESLFIINSSGDVFLEKHWRSVISKGICDYFLERLKNSNDVVPIIPTSMNSTNLVSINRC
GVYFVTVCKSEISPLFVIEFLHRVVDIFVDYFNECNETVIKENYVVIYELLDEMLDNGFP
LATESNVLKELIKPPNVFRTIANSVTGKTNFSDTLPVGSLSAIPWRKSGVKYTNNEAYFD
VIEEVDAIIDKSGSTIFAEISGEIQCLIKLSGMPDLSLSFVNPRILDDVSFHPCVRFKRW
ETERVLSFIPPDGGFRLMSYHVTSQSVPIPIYLRHVSEQGRLDITVGPKTTLGRTLESVK
LEILFPKSVVNCSLVTTQGKYVFDQNSKILNWDVGKIDVQKLPNIRGSVTVMAGTTIESM
PSINVQFTISQLAVSGLKVNRLDMYGDVKYKPFKGVKYVTKAGKFQIRL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g14458.t4 | CDD | cd14837 | AP3_Mu_N | 2 | 137 | 6.0985E-64 |
| 10 | g14458.t4 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 138 | 6.7E-43 |
| 11 | g14458.t4 | Gene3D | G3DSA:2.60.40.1170 | - | 164 | 404 | 4.7E-87 |
| 12 | g14458.t4 | Gene3D | G3DSA:2.60.40.1170 | - | 269 | 407 | 4.7E-87 |
| 3 | g14458.t4 | PANTHER | PTHR10529:SF342 | AP-3 COMPLEX SUBUNIT MU-1 | 4 | 408 | 9.4E-185 |
| 4 | g14458.t4 | PANTHER | PTHR10529 | AP COMPLEX SUBUNIT MU | 4 | 408 | 9.4E-185 |
| 13 | g14458.t4 | PIRSF | PIRSF005992 | AP_complex_mu | 1 | 409 | 4.9E-110 |
| 6 | g14458.t4 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 11 | 31 | 3.3E-24 |
| 7 | g14458.t4 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 97 | 124 | 3.3E-24 |
| 5 | g14458.t4 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 226 | 253 | 3.3E-24 |
| 2 | g14458.t4 | Pfam | PF01217 | Clathrin adaptor complex small chain | 3 | 126 | 8.6E-8 |
| 1 | g14458.t4 | Pfam | PF00928 | Adaptor complexes medium subunit family | 163 | 408 | 1.5E-70 |
| 16 | g14458.t4 | ProSitePatterns | PS00990 | Clathrin adaptor complexes medium chain signature 1. | 163 | 183 | - |
| 15 | g14458.t4 | ProSitePatterns | PS00991 | Clathrin adaptor complexes medium chain signature 2. | 246 | 260 | - |
| 17 | g14458.t4 | ProSiteProfiles | PS51072 | Mu homology domain (MHD) profile. | 174 | 408 | 37.497 |
| 8 | g14458.t4 | SUPERFAMILY | SSF64356 | SNARE-like | 2 | 137 | 5.49E-35 |
| 9 | g14458.t4 | SUPERFAMILY | SSF49447 | Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 163 | 408 | 5.89E-75 |
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 K12398 (AP-3 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.
