Gene loci information

Transcript annotation

  • This transcript has been annotated as AP-1 complex subunit mu-1.

Parent gene

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.t3 TSS g15819.t3 6873691 6873691
chr_4 g15819 g15819.t3 isoform g15819.t3 6874219 6876786
chr_4 g15819 g15819.t3 exon g15819.t3.exon1 6874219 6874859
chr_4 g15819 g15819.t3 cds g15819.t3.CDS1 6874335 6874859
chr_4 g15819 g15819.t3 exon g15819.t3.exon2 6874917 6875190
chr_4 g15819 g15819.t3 cds g15819.t3.CDS2 6874917 6875190
chr_4 g15819 g15819.t3 exon g15819.t3.exon3 6875431 6876786
chr_4 g15819 g15819.t3 cds g15819.t3.CDS3 6875431 6875654
chr_4 g15819 g15819.t3 TTS g15819.t3 NA NA

Sequences

>g15819.t3 Gene=g15819 Length=2271
GAATAGTAACACCAATAATTCAAACTGCCGAATGTACATTCGCCTATATAAAAACCAATA
ATCTCTACATTGTATCAACAACAAAAAAGAATGCAAATATTGCACTTGTTTTTACAATGC
TTCATAAAATTGTTCAAGTTTTTACTGAATATTTTAAAGAACTTGAAGAAGAATCAATTC
GTGATAATTTTGTAATAATTTATGAACTTCTTGATGAACTTATTGATTTTGGTTATCCAC
AAACAACAGATAGTAAAATTTTACAAGAATACATCACACAAGAAGGACATAAACTTGAAA
TTCAACCTCGAATTCCAATGGCTGTCACAAATGCCGTTTCATGGCGTTCAGAAGGAATAA
AATATCGTAAAAATGAAGTTTTTTTGGATGTCATTGAAAGTGTAAACCTTTTGGCAAATG
CAAATGGAAATGTTTTACGTAGTGAAATTGTTGGTGCAATAAAAATGCGAGTTTATCTTT
CGGGCATGCCAGAATTACGTCTTGGTCTCAATGACAAAGTCCTTTTTGAGTCAACTGGTC
GTGGCAAGTCAAAATCAATTGAACTTGAAGATGTCAAATTTCATCAATGTGTTCGACTTT
CACGATTTGAAAATGACAGGACAATTTCTTTTATACCACCGGATGGTGAATTTGAGCTCA
TGACCTACCGTAATAGTGCACATATGAAACCACTTATTTGGATTGAATCTGTGATTGAAA
GACATGCACATAGTCGAGTTGAGTACATGATCAAGGCAAAATCACAATTTAAAAGGCGTT
CGACAGCAAACAATGTCGAAATTATTATTCCTGTACCAAATGATGCTGACAGTCCTAAAT
TTAAAACTACTATTGGAAGTGTGAAATATACACCAGAACAGAGTGCTGTTACGTGGAGTA
TTAAATCTTTTCCTGGTGGAAAAGAATTTCTAATGCGAGCACATTTTGGTCTACCATCAG
TTGAATGTGAAGACAGCGAAGGAAAGCCACCAATTCAAGTTAAATTTGAGATTCCTTATT
TTACAACATCTGGAATTCAAGTAAGATATTTAAAAATTATTGAAAAAAGTGGATATCAGG
CATTACCTTGGGTTAGATATATTACACAAAATGGTGATTATCAATTGCGAACTAATTAAA
ATAGAATTTAGGATTTTTATATATTTCATATTTATTTTTTGATATATTCATAATTTACAA
TCTAGTTTTACAAAAAAATAAAATTTAGTTCATTTATTATCTATTATTTTATTTACCTTT
CAAAATGAATGACAAATTTTGACCTTAAGAAGGTCATGTTGAAAATTTGACTTTTGTGAT
GATAAATTAAATTTTTTGGAAAATTAACTAAAATTTCGATCAACATATGAAAACTTTCTG
ATTTTGTATTAATTTGTTTAAAAAAATTAAAAACTTAACCTAAGAACTTTTGACATTGCT
AAAACAAAAAATGATATACACTATTAGTGTTTAGTCAAGTTCAAAATTTTTAAAATATTC
AATTTGGATTTACACTAACTGCCAATAAATTTTAGATAAAATGGACTACAGTCTTCTCTC
GGATATAAGGAATAGTTCTTGTATTCGAATCAAAACATGACATATTTAACAATGTAAAAA
TTTTTAAAAACTGTTAAATTTTTTTAAAAAAAAATCTGGTAAATTTTTAAACTTACAAAG
AAAATCATTATTTTTTAACGGTTTTTTCAAATGCGTTTCTTGTATTCAAATTTCTTTCTA
TACAAAACAAAAACCAAATTTTCGGAAAAATTTTCAATCAAATTCAAAAATTTTATTTCC
GAGGGAAGAATTTTAATGTTTTATTGACATTTCTGAAAACAACTCAAAATAATTTGAACC
GAAATGTATGTCAAAGTTCTGTTTAAAATTTTCTATAGAAATTCATCTTTGATTATTTGA
GTAATAAATTTTCCAATAATCTTCAACTTTTATGTTCAAAAAATTGTCTAAAAATTTAAA
GTGTTGATTAAATATAAAACTTAAAACATTGAAAAGACTCAATCAAGACAAGAATTTAAA
ACTTGAATAAATTTTTTTAATGAAATTAAAAATTTCAAGTGCTAAAATTATAAACGAAAT
AAATTTTGTACAAAATGACAAGTAGTTATTAGAGTAAGAAACTATTTAATCATTTCAATT
AATATTTATTACCATAATTATTAATTATTTTTGCACATAAAATTATTTTGCTTAACACTT
ATAAAATTATTTTTATGTAAACAAAAATAAATAAAATATTTGTTTTAAAAT

>g15819.t3 Gene=g15819 Length=340
MLHKIVQVFTEYFKELEEESIRDNFVIIYELLDELIDFGYPQTTDSKILQEYITQEGHKL
EIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESVNLLANANGNVLRSEIVGAIKMRVY
LSGMPELRLGLNDKVLFESTGRGKSKSIELEDVKFHQCVRLSRFENDRTISFIPPDGEFE
LMTYRNSAHMKPLIWIESVIERHAHSRVEYMIKAKSQFKRRSTANNVEIIIPVPNDADSP
KFKTTIGSVKYTPEQSAVTWSIKSFPGGKEFLMRAHFGLPSVECEDSEGKPPIQVKFEIP
YFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g15819.t3 CDD cd09258 AP-1_Mu1A_Cterm 70 339 0.0
11 g15819.t3 Gene3D G3DSA:3.30.450.60 - 1 61 3.7E-25
12 g15819.t3 Gene3D G3DSA:2.60.40.1170 - 81 334 9.6E-113
13 g15819.t3 Gene3D G3DSA:2.60.40.1170 - 192 338 9.6E-113
2 g15819.t3 PANTHER PTHR10529:SF257 AP-1 COMPLEX SUBUNIT MU-1 2 339 8.7E-208
3 g15819.t3 PANTHER PTHR10529 AP COMPLEX SUBUNIT MU 2 339 8.7E-208
14 g15819.t3 PIRSF PIRSF005992 AP_complex_mu 1 340 8.3E-127
5 g15819.t3 PRINTS PR00314 Clathrin coat assembly protein signature 18 45 5.2E-57
7 g15819.t3 PRINTS PR00314 Clathrin coat assembly protein signature 76 104 5.2E-57
8 g15819.t3 PRINTS PR00314 Clathrin coat assembly protein signature 150 177 5.2E-57
6 g15819.t3 PRINTS PR00314 Clathrin coat assembly protein signature 219 234 5.2E-57
4 g15819.t3 PRINTS PR00314 Clathrin coat assembly protein signature 259 270 5.2E-57
1 g15819.t3 Pfam PF00928 Adaptor complexes medium subunit family 74 338 7.5E-91
17 g15819.t3 ProSitePatterns PS00990 Clathrin adaptor complexes medium chain signature 1. 74 94 -
16 g15819.t3 ProSitePatterns PS00991 Clathrin adaptor complexes medium chain signature 2. 170 184 -
18 g15819.t3 ProSiteProfiles PS51072 Mu homology domain (MHD) profile. 85 338 46.706
9 g15819.t3 SUPERFAMILY SSF64356 SNARE-like 1 58 1.24E-19
10 g15819.t3 SUPERFAMILY SSF49447 Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor 74 338 2.35E-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 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.

Raw TPM values