General information for g5612.t1
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 g5612 is located on chr_2: 10605463..10606853 (+ 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_2 | g5612 | g5612.t1 | TSS | g5612.t1 | 10603910 | 10603910 |
| chr_2 | g5612 | g5612.t1 | isoform | g5612.t1 | 10603977 | 10605463 |
| chr_2 | g5612 | g5612.t1 | exon | g5612.t1.exon1 | 10603977 | 10604094 |
| chr_2 | g5612 | g5612.t1 | cds | g5612.t1.CDS1 | 10603977 | 10604094 |
| chr_2 | g5612 | g5612.t1 | exon | g5612.t1.exon2 | 10604316 | 10605463 |
| chr_2 | g5612 | g5612.t1 | cds | g5612.t1.CDS2 | 10604316 | 10605463 |
| chr_2 | g5612 | g5612.t1 | TTS | g5612.t1 | 10605558 | 10605558 |
Sequences
>g5612.t1 Gene=g5612 Length=1266
ATGTTTAGTCAAATATTTATTTTGGACCTTAAAGGCAAAGTTCTCATATCTCGTAATTAT
CGAGGGGAGCTAGATTCGACAGTAATTGACCGATTCATGCCCTATTTGATGGATAGAGAG
GAAGAAGGAACTGTTAGTCCGCTACTTCAAACACAAGATTGCACTTTTGCTTACATCAAA
ACAAGTAACTTATATATTGTAACAACTACAAGACGAAATGCAAATATTGCTTTAATTTTT
ACAATGTTACATAAAATTGTTGAAGTTTTTACTGAATATTTCAAAGAACTCGAAGAAGAA
TCGATTCGTGACAATTTTGTCATCATTTATGAGCTTCTAGATGAACTCATTGATTTTGGC
TATCCGCAGACCACAGATAGTAAAATTCTTCAAGAGTATATTACTCAGGAAGGCTATAAA
CTTGAAATTCAACCGCGCATTCCAATGGCAGTTACAAATGCAGTCTCATGGCGTTCAGAA
GGTATCAAATATCGTAAAAATGAAGTATTTTTGGATGTAATCGAAAGTGTTAATCTTTTG
GCAAATCAAAATGGAACAGTATTGCGAAGTGAAATTGAAGGTGCAATAAAAATGAGAGTA
TATCTATCAGGCATGCCAGAACTTCGTCTGGGATTAAATGATAAAGTATTATTTGAGAGC
ACTGGTCGTGGAAAATCTAAATCCATTGAGCTTGAAGATGTCAAATTTCATCAATGCGTA
CGATTATCGCGTTTTGAAAATGACAGAACGATTTCTTTTGTGCCGCCAGATGGAGAATTT
GAGCTCATGACCTACCGCAACAGTAATCAAATAAAACCTTTAATTTGGATTGAATCAGTT
ATTGAAAGACACGCTCATAGTCGTATTGAGTATATGATAAAAGCTAAATCACAATTCAAA
CGTCGCTCTACCGCGAATAATGTTGAAATTATCATTCCAGTACCATGTGATGCAGATTCA
CCTAAATTTAAAACAACTATTGGTAATGTGAAATATAATCCTGAACAAAATGCTATTGTA
TGGAATATCAAGAGTTTTCCAGGTGGAAAGGAATTTTTAATGCGTGCACAATTTCAATTG
CCTTCTGTTCAAAGTGAAGATGTTGAAGGAAAGCCACCAATACAAGTTCGTTTCGAAATT
CCTTATTTTACAGTTTCTGGAATTCAAGTCAGATATTTGAAGATTATTGAAAAAAGTGGC
TATCAAGCTCTCCCTTGGGTACGATATATAACACAGAATGGTGATTATCAATTAAGAACA
AATTAA
>g5612.t1 Gene=g5612 Length=421
MFSQIFILDLKGKVLISRNYRGELDSTVIDRFMPYLMDREEEGTVSPLLQTQDCTFAYIK
TSNLYIVTTTRRNANIALIFTMLHKIVEVFTEYFKELEEESIRDNFVIIYELLDELIDFG
YPQTTDSKILQEYITQEGYKLEIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESVNLL
ANQNGTVLRSEIEGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKSKSIELEDVKFHQCV
RLSRFENDRTISFVPPDGEFELMTYRNSNQIKPLIWIESVIERHAHSRIEYMIKAKSQFK
RRSTANNVEIIIPVPCDADSPKFKTTIGNVKYNPEQNAIVWNIKSFPGGKEFLMRAQFQL
PSVQSEDVEGKPPIQVRFEIPYFTVSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRT
N
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5612.t1 | CDD | cd14835 | AP1_Mu_N | 3 | 141 | 1.47554E-87 |
| 18 | g5612.t1 | CDD | cd09258 | AP-1_Mu1A_Cterm | 151 | 420 | 0.0 |
| 13 | g5612.t1 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 142 | 2.8E-52 |
| 14 | g5612.t1 | Gene3D | G3DSA:2.60.40.1170 | - | 162 | 415 | 2.3E-113 |
| 15 | g5612.t1 | Gene3D | G3DSA:2.60.40.1170 | - | 273 | 419 | 2.3E-113 |
| 3 | g5612.t1 | PANTHER | PTHR10529:SF257 | AP-1 COMPLEX SUBUNIT MU-1 | 3 | 420 | 1.4E-229 |
| 4 | g5612.t1 | PANTHER | PTHR10529 | AP COMPLEX SUBUNIT MU | 3 | 420 | 1.4E-229 |
| 16 | g5612.t1 | PIRSF | PIRSF005992 | AP_complex_mu | 1 | 421 | 1.7E-145 |
| 8 | g5612.t1 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 12 | 32 | 1.6E-67 |
| 10 | g5612.t1 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 99 | 126 | 1.6E-67 |
| 7 | g5612.t1 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 157 | 185 | 1.6E-67 |
| 6 | g5612.t1 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 231 | 258 | 1.6E-67 |
| 9 | g5612.t1 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 300 | 315 | 1.6E-67 |
| 5 | g5612.t1 | PRINTS | PR00314 | Clathrin coat assembly protein signature | 340 | 351 | 1.6E-67 |
| 2 | g5612.t1 | Pfam | PF01217 | Clathrin adaptor complex small chain | 2 | 130 | 7.7E-10 |
| 1 | g5612.t1 | Pfam | PF00928 | Adaptor complexes medium subunit family | 155 | 419 | 2.8E-93 |
| 19 | g5612.t1 | ProSitePatterns | PS00990 | Clathrin adaptor complexes medium chain signature 1. | 155 | 175 | - |
| 20 | g5612.t1 | ProSiteProfiles | PS51072 | Mu homology domain (MHD) profile. | 166 | 419 | 47.046 |
| 11 | g5612.t1 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 139 | 1.35E-41 |
| 12 | g5612.t1 | SUPERFAMILY | SSF49447 | Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 155 | 419 | 1.15E-100 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5612/g5612.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5612.t1.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 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.
