General information for g3706.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AP-1 complex subunit beta-1.
Parent gene
- The parent gene g3706 is located on chr_3: 27565913..27568405 (+ 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_3 | g3706 | g3706.t1 | TSS | g3706.t1 | 27564681 | 27564681 |
| chr_3 | g3706 | g3706.t1 | isoform | g3706.t1 | 27565122 | 27568405 |
| chr_3 | g3706 | g3706.t1 | exon | g3706.t1.exon1 | 27565122 | 27565144 |
| chr_3 | g3706 | g3706.t1 | cds | g3706.t1.CDS1 | 27565122 | 27565144 |
| chr_3 | g3706 | g3706.t1 | exon | g3706.t1.exon2 | 27565208 | 27565514 |
| chr_3 | g3706 | g3706.t1 | cds | g3706.t1.CDS2 | 27565208 | 27565514 |
| chr_3 | g3706 | g3706.t1 | exon | g3706.t1.exon3 | 27565913 | 27568405 |
| chr_3 | g3706 | g3706.t1 | cds | g3706.t1.CDS3 | 27565913 | 27568405 |
| chr_3 | g3706 | g3706.t1 | TTS | g3706.t1 | 27568620 | 27568620 |
Sequences
>g3706.t1 Gene=g3706 Length=2823
ATGATTCCCATTGCGGCAATTCAAATAAGAGCTTTTGATAGAGATCACGGAATGACTGAC
TCAAAGTATTTTACAACCACCAAGAAAGGTGAAATCTTCGAGCTAAAATCAGAGCTTAAT
AGTGACAAAAAGGAAAAGAAAAAAGAAGCTGTAAAGAAAGTCATTGCAAGTATGACTGTT
GGCAAAGATGTTTCAGCATTATTTCCTGATGTTGTCAACTGTATGCAAACAGATAATCTT
GAACTTAAGAAGCTTGTCTATCTTTATCTCATGAATTATGCCAAGTCACAGCCTGACATG
GCAATTATGGCTGTCAATACTTTCGTTAAGGATTGCGAAGATTCAAATCCGTTGATAAGA
GCGTTGGCTGTCAGAACAATGGGATGTATTCGTGTCGATAAAATTACTGAATATTTATGT
GAACCATTGAGAAAGTGTTTAAAAGATGAAGATCCGTATGTTCGTAAAACTGCCGCTGTA
TGTGTTGCTAAATTATATGATATTTCAAGCTCGATGGTTGAAGATCAAGGCTTTTTGGAT
CAATTGAAAGATTTACTGTCAGATTCAAATCCAATGGTTGTTGCAAATGCTGTTGCTGCT
TTAAGTGAGATTAATGAATCGTCAGCATCTGGTCAACCACTTGTTGAATTGAATTCAGCA
ACAATTAATAAGCTTCTTACTGCTCTCAATGAATGTACTGAATGGGGTCAAGTTTTTATT
CTCGATTCATTAGCAAATTATACACCAAAAGATGAACGTGAAGCACAATCAATTTGTGAA
AGAATTACACCACGTCTTGCTCATGCAAATGCTGCTGTTGTCTTAAGTGCAATCAAAGTG
TTGATGAAGTTGCTCGAAATTTTATCATCTGATAGTGATTTCTGTGCTACATTGACTAAA
AAGCTTGCACCACCACTTGTTACTCTTCTTTCATCCGAAGCAGAGGTACAATATGTAGCA
TTGAGAAATATCAATTTGATTGTTCAAAAACGTCCTGATATTTTGAAACATGAGATGAAA
GTTTTCTTCGTCAAATATAATGATCCAATTTATGTGAAACTCGAGAAATTGGATATCATG
ATTCGTTTGGCAAATCAAAGTAATATTGCACAAGTTTTGAGTGAATTAAAAGAATATGCA
ACAGAAGTTGATGTTGATTTTGTTCGTAAAGCAGTAAGAGCTATTGGTCGCTGTGCAATA
AAAGTTGAGCCATCTGCTGAACGATGTGTTTCAACATTACTTGAATTAATTCAAACTAAA
GTCAACTATGTGGTTCAAGAAGCTATTGTTGTTATTAAAGATATCTTTAGAAAATATCCA
AATAAATATGAAAGCATCATTAGTACATTGTGTGAGAATTTGGATACACTTGATGAGCCT
GAAGCTCGAGCATCGATGGTATGGATTATTGGTGAATATGCAGAAAGAATTGACAATGCT
GATGAGTTGCTTGATAGCTTTTTGGAAGGATTCCAAGATGAGAATGCTCAAGTGCAGTTG
CAGCTTTTGACAGCTGTTGTAAAATTATTTCTTAAACGACCAGCTGATACACAAGAATTG
GTTCAACATGTTTTATCTCTCGCTACACAAGATAGTGATAACCCTGATTTGCGAGATCGA
GGTTTCATTTACTGGCGTTTATTATCAACAGATCCAGCAGCTGCAAAAGAAGTAGTTTTG
GCTGATAAACCATTAATTTCTGAGGAAACTGATTTATTGGAACCAACACTACTCGATGAA
TTGATTTGTCATATTGCATCATTGGCAAGTGTTTACCATAAGCCGCCAACAGCATTTGTT
GAAGGTCGTACAGCTGGTGTTCGTAAATCACTTCCTAATCGTACCATTCCAAGTGCTAGT
GATCATGATAATAATGTCGAAGCAACAGTAATTCCAAGTCAAGACTCATTAATTGGTGAT
CTTTTGTCAATGGATATTGGAGATATTAATGCACCTGCTCCTGCTTCATCTGTAATTCCT
CAACAGCACAGCAATGTTGATTTACTTGGTGGTGGTCTTGATATTTTATTAGGTGGTCCC
GCACCAACAGCAGTCGAACCCGCAACTTTAAATACCGGTAATGGACTCCTCGGCGATATT
TTCGGTCTCAGTACACCTGCAACAACAATGGTTTCAGTGCCGAAAATTACATGGCTGCCT
GCAGAAAAAGGCAAAGGCTTAGAAATTCAAGGAACATTTGCTAGACGAGGAGGACATGTA
TTTATGGACATGACATTCACAAACAAAGCAATGCAAGCTATGAGTGGCTTTGCTATACAA
TTTAATAAAAATAGTTTCGGTCTTGTGCCAGGTGCTCCTCTTCAAGTTCCAACATTACCT
CCAGCTCAATCGACAGAAGTTTCTCTTCAACTCAACAACACTGGACCAGTCTTGAGAATG
GAACCAATTAATAATCTTCAAATCGCTATTAAAAATAATGTTGATGTTTTCTATTTTGCA
TGTTTGGTACATGGACAAACATTATTCTCGGAAGAAGGACAATTAGACAAAAGAGTTTTC
TTATCAACTTGGAAAGAAATTCCAGCAGCTAATGAAGTTCAATACACTCTAAGTGGAATT
ATTGGAAATGCTGATGGTGTTGCACAAAAAATGACAGCCAATAATGTATTTACAATCGCA
AAGAGAAATGTCGAAGGGCAGGATATGCTATACCAATCACTCAAACTCGACAATAATGTT
TGGGTTCTACTTGAATTGAAACTCACACCAGGAAGTACAGAAGGAACACTCAGCTTGAAA
ACAAGATCTGTTGAAGTCGCTCAAATGGTCTTTACTGCTTATGAAATTATAATAAAATCT
TAA
>g3706.t1 Gene=g3706 Length=940
MIPIAAIQIRAFDRDHGMTDSKYFTTTKKGEIFELKSELNSDKKEKKKEAVKKVIASMTV
GKDVSALFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDSNPLIR
ALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLYDISSSMVEDQGFLD
QLKDLLSDSNPMVVANAVAALSEINESSASGQPLVELNSATINKLLTALNECTEWGQVFI
LDSLANYTPKDEREAQSICERITPRLAHANAAVVLSAIKVLMKLLEILSSDSDFCATLTK
KLAPPLVTLLSSEAEVQYVALRNINLIVQKRPDILKHEMKVFFVKYNDPIYVKLEKLDIM
IRLANQSNIAQVLSELKEYATEVDVDFVRKAVRAIGRCAIKVEPSAERCVSTLLELIQTK
VNYVVQEAIVVIKDIFRKYPNKYESIISTLCENLDTLDEPEARASMVWIIGEYAERIDNA
DELLDSFLEGFQDENAQVQLQLLTAVVKLFLKRPADTQELVQHVLSLATQDSDNPDLRDR
GFIYWRLLSTDPAAAKEVVLADKPLISEETDLLEPTLLDELICHIASLASVYHKPPTAFV
EGRTAGVRKSLPNRTIPSASDHDNNVEATVIPSQDSLIGDLLSMDIGDINAPAPASSVIP
QQHSNVDLLGGGLDILLGGPAPTAVEPATLNTGNGLLGDIFGLSTPATTMVSVPKITWLP
AEKGKGLEIQGTFARRGGHVFMDMTFTNKAMQAMSGFAIQFNKNSFGLVPGAPLQVPTLP
PAQSTEVSLQLNNTGPVLRMEPINNLQIAIKNNVDVFYFACLVHGQTLFSEEGQLDKRVF
LSTWKEIPAANEVQYTLSGIIGNADGVAQKMTANNVFTIAKRNVEGQDMLYQSLKLDNNV
WVLLELKLTPGSTEGTLSLKTRSVEVAQMVFTAYEIIIKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g3706.t1 | Gene3D | G3DSA:1.25.10.10 | - | 18 | 609 | 0 |
| 13 | g3706.t1 | Gene3D | G3DSA:2.60.40.1150 | - | 711 | 824 | 0 |
| 11 | g3706.t1 | Gene3D | G3DSA:3.30.310.10 | - | 826 | 940 | 0 |
| 4 | g3706.t1 | PANTHER | PTHR11134:SF31 | AP-1 COMPLEX SUBUNIT BETA-1 | 18 | 938 | 0 |
| 5 | g3706.t1 | PANTHER | PTHR11134 | ADAPTOR COMPLEX SUBUNIT BETA FAMILY MEMBER | 18 | 938 | 0 |
| 14 | g3706.t1 | PIRSF | PIRSF002291 | Beta_adaptin | 14 | 772 | 0 |
| 3 | g3706.t1 | Pfam | PF01602 | Adaptin N terminal region | 32 | 550 | 0 |
| 1 | g3706.t1 | Pfam | PF02883 | Adaptin C-terminal domain | 718 | 819 | 0 |
| 2 | g3706.t1 | Pfam | PF09066 | Beta2-adaptin appendage, C-terminal sub-domain | 831 | 937 | 0 |
| 10 | g3706.t1 | SMART | SM00809 | alpha_adaptinc2 | 714 | 820 | 0 |
| 9 | g3706.t1 | SMART | SM01020 | B2_adapt_app_C_2 | 829 | 939 | 0 |
| 6 | g3706.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 23 | 597 | 0 |
| 7 | g3706.t1 | SUPERFAMILY | SSF49348 | Clathrin adaptor appendage domain | 711 | 824 | 0 |
| 8 | g3706.t1 | SUPERFAMILY | SSF55711 | Subdomain of clathrin and coatomer appendage domain | 828 | 939 | 0 |
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:0030117 | membrane coat | CC |
| GO:0030276 | clathrin binding | MF |
| GO:0030131 | clathrin adaptor complex | CC |
| GO:0015031 | protein transport | BP |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K12392 (AP-1 complex subunit beta-1)
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.
