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.t1 TSS g15819.t1 6873691 6873691
chr_4 g15819 g15819.t1 isoform g15819.t1 6873803 6875654
chr_4 g15819 g15819.t1 exon g15819.t1.exon1 6873803 6873920
chr_4 g15819 g15819.t1 cds g15819.t1.CDS1 6873803 6873920
chr_4 g15819 g15819.t1 exon g15819.t1.exon2 6874210 6874859
chr_4 g15819 g15819.t1 cds g15819.t1.CDS2 6874210 6874859
chr_4 g15819 g15819.t1 exon g15819.t1.exon3 6874917 6875190
chr_4 g15819 g15819.t1 cds g15819.t1.CDS3 6874917 6875190
chr_4 g15819 g15819.t1 exon g15819.t1.exon4 6875431 6875654
chr_4 g15819 g15819.t1 cds g15819.t1.CDS4 6875431 6875654
chr_4 g15819 g15819.t1 TTS g15819.t1 NA NA

Sequences

>g15819.t1 Gene=g15819 Length=1266
ATGATCTTTCAAATTTTTCTCCTCGATGTCAAAGGAAAAGTTTTGGTATCGAGAAATTAT
CGAGGTGAAATTGATTCATCAGTGATTGATAAATTTATGCCAATGCTCATGGAAAAAGAG
GAAGAAGGAATAGTAACACCAATAATTCAAACTGCCGAATGTACATTCGCCTATATAAAA
ACCAATAATCTCTACATTGTATCAACAACAAAAAAGAATGCAAATATTGCACTTGTTTTT
ACAATGCTTCATAAAATTGTTCAAGTTTTTACTGAATATTTTAAAGAACTTGAAGAAGAA
TCAATTCGTGATAATTTTGTAATAATTTATGAACTTCTTGATGAACTTATTGATTTTGGT
TATCCACAAACAACAGATAGTAAAATTTTACAAGAATACATCACACAAGAAGGACATAAA
CTTGAAATTCAACCTCGAATTCCAATGGCTGTCACAAATGCCGTTTCATGGCGTTCAGAA
GGAATAAAATATCGTAAAAATGAAGTTTTTTTGGATGTCATTGAAAGTGTAAACCTTTTG
GCAAATGCAAATGGAAATGTTTTACGTAGTGAAATTGTTGGTGCAATAAAAATGCGAGTT
TATCTTTCGGGCATGCCAGAATTACGTCTTGGTCTCAATGACAAAGTCCTTTTTGAGTCA
ACTGGTCGTGGCAAGTCAAAATCAATTGAACTTGAAGATGTCAAATTTCATCAATGTGTT
CGACTTTCACGATTTGAAAATGACAGGACAATTTCTTTTATACCACCGGATGGTGAATTT
GAGCTCATGACCTACCGTAATAGTGCACATATGAAACCACTTATTTGGATTGAATCTGTG
ATTGAAAGACATGCACATAGTCGAGTTGAGTACATGATCAAGGCAAAATCACAATTTAAA
AGGCGTTCGACAGCAAACAATGTCGAAATTATTATTCCTGTACCAAATGATGCTGACAGT
CCTAAATTTAAAACTACTATTGGAAGTGTGAAATATACACCAGAACAGAGTGCTGTTACG
TGGAGTATTAAATCTTTTCCTGGTGGAAAAGAATTTCTAATGCGAGCACATTTTGGTCTA
CCATCAGTTGAATGTGAAGACAGCGAAGGAAAGCCACCAATTCAAGTTAAATTTGAGATT
CCTTATTTTACAACATCTGGAATTCAAGTAAGATATTTAAAAATTATTGAAAAAAGTGGA
TATCAGGCATTACCTTGGGTTAGATATATTACACAAAATGGTGATTATCAATTGCGAACT
AATTAA

>g15819.t1 Gene=g15819 Length=421
MIFQIFLLDVKGKVLVSRNYRGEIDSSVIDKFMPMLMEKEEEGIVTPIIQTAECTFAYIK
TNNLYIVSTTKKNANIALVFTMLHKIVQVFTEYFKELEEESIRDNFVIIYELLDELIDFG
YPQTTDSKILQEYITQEGHKLEIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESVNLL
ANANGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKSKSIELEDVKFHQCV
RLSRFENDRTISFIPPDGEFELMTYRNSAHMKPLIWIESVIERHAHSRVEYMIKAKSQFK
RRSTANNVEIIIPVPNDADSPKFKTTIGSVKYTPEQSAVTWSIKSFPGGKEFLMRAHFGL
PSVECEDSEGKPPIQVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRT
N

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g15819.t1 CDD cd14835 AP1_Mu_N 5 141 1.45996E-88
18 g15819.t1 CDD cd09258 AP-1_Mu1A_Cterm 151 420 0.0
13 g15819.t1 Gene3D G3DSA:3.30.450.60 - 1 142 3.9E-52
14 g15819.t1 Gene3D G3DSA:2.60.40.1170 - 162 415 1.9E-112
15 g15819.t1 Gene3D G3DSA:2.60.40.1170 - 273 419 1.9E-112
3 g15819.t1 PANTHER PTHR10529:SF257 AP-1 COMPLEX SUBUNIT MU-1 5 420 2.2E-240
4 g15819.t1 PANTHER PTHR10529 AP COMPLEX SUBUNIT MU 5 420 2.2E-240
16 g15819.t1 PIRSF PIRSF005992 AP_complex_mu 1 421 7.0E-144
8 g15819.t1 PRINTS PR00314 Clathrin coat assembly protein signature 12 32 1.1E-67
10 g15819.t1 PRINTS PR00314 Clathrin coat assembly protein signature 99 126 1.1E-67
7 g15819.t1 PRINTS PR00314 Clathrin coat assembly protein signature 157 185 1.1E-67
6 g15819.t1 PRINTS PR00314 Clathrin coat assembly protein signature 231 258 1.1E-67
9 g15819.t1 PRINTS PR00314 Clathrin coat assembly protein signature 300 315 1.1E-67
5 g15819.t1 PRINTS PR00314 Clathrin coat assembly protein signature 340 351 1.1E-67
2 g15819.t1 Pfam PF01217 Clathrin adaptor complex small chain 1 132 7.9E-8
1 g15819.t1 Pfam PF00928 Adaptor complexes medium subunit family 155 419 1.5E-90
20 g15819.t1 ProSitePatterns PS00990 Clathrin adaptor complexes medium chain signature 1. 155 175 -
19 g15819.t1 ProSitePatterns PS00991 Clathrin adaptor complexes medium chain signature 2. 251 265 -
21 g15819.t1 ProSiteProfiles PS51072 Mu homology domain (MHD) profile. 166 419 46.706
11 g15819.t1 SUPERFAMILY SSF64356 SNARE-like 1 139 2.2E-41
12 g15819.t1 SUPERFAMILY SSF49447 Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor 155 419 4.58E-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

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.

Raw TPM values