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_2 g5612 g5612.t4 TSS g5612.t4 10603910 10603910
chr_2 g5612 g5612.t4 isoform g5612.t4 10604635 10605463
chr_2 g5612 g5612.t4 exon g5612.t4.exon1 10604635 10605179
chr_2 g5612 g5612.t4 cds g5612.t4.CDS1 10604642 10605179
chr_2 g5612 g5612.t4 exon g5612.t4.exon2 10605230 10605463
chr_2 g5612 g5612.t4 cds g5612.t4.CDS2 10605230 10605294
chr_2 g5612 g5612.t4 TTS g5612.t4 10605558 10605558

Sequences

>g5612.t4 Gene=g5612 Length=779
CATTCCAATGGCAGTTACAAATGCAGTCTCATGGCGTTCAGAAGGTATCAAATATCGTAA
AAATGAAGTATTTTTGGATGTAATCGAAAGTGTTAATCTTTTGGCAAATCAAAATGGAAC
AGTATTGCGAAGTGAAATTGAAGGTGCAATAAAAATGAGAGTATATCTATCAGGCATGCC
AGAACTTCGTCTGGGATTAAATGATAAAGTATTATTTGAGAGCACTGGTCGTGGAAAATC
TAAATCCATTGAGCTTGAAGATGTCAAATTTCATCAATGCGTACGATTATCGCGTTTTGA
AAATGACAGAACGATTTCTTTTGTGCCGCCAGATGGAGAATTTGAGCTCATGACCTACCG
CAACAGTAATCAAATAAAACCTTTAATTTGGATTGAATCAGTTATTGAAAGACACGCTCA
TAGTCGTATTGAGTATATGATAAAAGCTAAATCACAATTCAAACGTCGCTCTACCGCGAA
TAATGTTGAAATTATCATTCCAGTACCATGTGATGCAGATTCACCTAAATTTAAAACAAC
TATTGAGTTTTCCAGGTGGAAAGGAATTTTTAATGCGTGCACAATTTCAATTGCCTTCTG
TTCAAAGTGAAGATGTTGAAGGAAAGCCACCAATACAAGTTCGTTTCGAAATTCCTTATT
TTACAGTTTCTGGAATTCAAGTCAGATATTTGAAGATTATTGAAAAAAGTGGCTATCAAG
CTCTCCCTTGGGTACGATATATAACACAGAATGGTGATTATCAATTAAGAACAAATTAA

>g5612.t4 Gene=g5612 Length=200
MAVTNAVSWRSEGIKYRKNEVFLDVIESVNLLANQNGTVLRSEIEGAIKMRVYLSGMPEL
RLGLNDKVLFESTGRGKSKSIELEDVKFHQCVRLSRFENDRTISFVPPDGEFELMTYRNS
NQIKPLIWIESVIERHAHSRIEYMIKAKSQFKRRSTANNVEIIIPVPCDADSPKFKTTIE
FSRWKGIFNACTISIAFCSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5612.t4 Gene3D G3DSA:2.60.40.1170 - 8 163 1.5E-58
2 g5612.t4 PANTHER PTHR10529:SF257 AP-1 COMPLEX SUBUNIT MU-1 2 186 1.6E-106
3 g5612.t4 PANTHER PTHR10529 AP COMPLEX SUBUNIT MU 2 186 1.6E-106
6 g5612.t4 PRINTS PR00314 Clathrin coat assembly protein signature 9 37 5.6E-36
5 g5612.t4 PRINTS PR00314 Clathrin coat assembly protein signature 83 110 5.6E-36
4 g5612.t4 PRINTS PR00314 Clathrin coat assembly protein signature 152 167 5.6E-36
1 g5612.t4 Pfam PF00928 Adaptor complexes medium subunit family 7 179 2.1E-60
8 g5612.t4 ProSitePatterns PS00990 Clathrin adaptor complexes medium chain signature 1. 7 27 -
10 g5612.t4 ProSiteProfiles PS51072 Mu homology domain (MHD) profile. 18 200 31.813
7 g5612.t4 SUPERFAMILY SSF49447 Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor 7 179 1.44E-64

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5612/g5612.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5612.t4.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.

Raw TPM values