General information for g1972.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Anaphase-promoting complex subunit 4.
Parent gene
- The parent gene g1972 is located on chr_3: 14156107..14161713 (+ 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 | g1972 | g1972.t9 | isoform | g1972.t9 | 14154000 | 14156285 |
| chr_3 | g1972 | g1972.t9 | exon | g1972.t9.exon1 | 14154000 | 14156285 |
| chr_3 | g1972 | g1972.t9 | cds | g1972.t9.CDS1 | 14154032 | 14156107 |
| chr_3 | g1972 | g1972.t9 | TTS | g1972.t9 | 14156355 | 14156355 |
| chr_3 | g1972 | g1972.t9 | TSS | g1972.t9 | NA | NA |
Sequences
>g1972.t9 Gene=g1972 Length=2286
GTGAAGTAACAATTAATAGATTTAAATGGGATATGCCGATTAAAATATTACCACCAGAAG
AAAAGATTGCTGTCAAGTCAATTTCATGGAGGATGGATGAAAGAATTATAGGAATAGCAT
ATAACAATCAACTTATAAATTTGGTTGATATTGAATCAAAAGAAGTAATCATTTCATACA
GTGTAAATGCAGATGTCACTAAAATTTGTTGGACTCAGAATTCAATAGATATAGATTCAA
ATGAAAAATCAATTCTAGATGATCATGTTTTTCTAGCTTCTTTGCCAAGTATCAATAGTA
CAATATCTTCCGGAACTAAAAAGAGTGACTACAATAGCACACGCTTCTACTCGAATACTG
GATTAAATTTTCTCATTGTAATCTGTAATGATTGTACAATAAGAGCCTACATATATGGTG
TTCTCTCATGTGGATCGATTGATGTTAAAAAGAAACTTAATGTAAATGAATCTGATTCAC
TGAATATAATAGAAGCAAAAATGAGTTCAAATTTCGAACGATTCTTTGTTGTTTATGTAA
AAAATGGCATTCTGGGAACTCTTGTTTTTGAGAATTCAGCTCTTCTTAAGCGACATGTTG
CATTGTGGAAACTATCGATCAAGTATGGAATGATATTAAATATTTTTGAATACATGGATG
ACACTATTGAACATATTAATGAAGCTTGGGAGTCAGTTTTACTTGAGATGGACAATAAAC
TATCAAAATATGCTAAAAAGCAAGAGGCAGGCTCAATTTCTGCAGACTTTTTGGAGTTAC
TACTCTTTGGATATCCATCTGAAGAATTAGAAAATTTTCTTACTCATGAAATGACTGTAA
GAGAATTGAAGAAACTCAGTAATAGTGTTGAAATGAGTTATAGTACAATACAAAAGCTCG
TTGTAAAACCACTACATAGTGCTATAATTTCAATATTCTATCATGTCAATAATCTTCATG
GAATGCATCAAAATGCATATGAATATAAAAATCTTTTGGGTGAGAATTCAAGTGAAGCGC
TTATTTCGACTGGATCGTTTCTCATAAAATCTCACGAATTACAACAAATTATTGATAAAT
CAATGAGAGATTTTAAAATTTTCTTTCGCTGGCTGTATATTGCAATTTCGAGATTAATGG
ATGACACAGTTCCTGATGATGCAGGAGTTATTACTCAGCAAGAAGTTAATTATTTGGCTG
AATTTTTATACAATTTCGAAGAGAATAGAAAAGAGTTGGTTCATGATGAGTCAGGTGAAA
AAGAGATAAAATTTAATTTGGAACGTGTTGGTCAATATTTAACAAATCAAAATCTTACAA
TTCCTTCTATCGATAACACTTCTAATATTTGGAATGAAATTTTCACACAAAATGAATGTT
TGCAAACCAGCAAATTGATTTATCCACACAATAAAGATTCATCTCTTATTCAAGAAAAAA
ATAAAATGGAGAAAAGTATCAAAGATTTATTCAATAGATTAGAGCATTCGATTGGTCAAG
AGTATAATTTGAAAAATGATTTTATAATTTCTCATTCTGATGACATTGCATCATCTACAA
TTGTCACTTCACACATAATCGATGGAGAGAATCAAGATGCAATTAATCTATTTACAATTT
TACTATCTGAGAAAGATTTATTGCTGCTCGTTTATTATTCCAATACATATATTCCAAAAA
TTGCCAAGTTACAATTTACAAATCGAGATGAATGCAATATTTTGTCTGTGGGACAGCTTT
CATTCATTGATATAAAATTTTACAACACGAGATTGCTATCAGGATTAATTAAGAATGAAA
TTGGAAACAAAATTCAAACATGCTTCATTCAAGTACCTGTATCACGTCTCATTGATGAGC
TACTCGAATATGATCAAAAAACCATTCCCACATTTAATATGTATAATTATATAGACGACT
GTAATTTTAAAGTCATTGAAGGTTTTGCAGGCAATTTAATGGCAGTGTCTGGGTCTCGAA
AAGTTGCAGCATTTTTGGCATCAAATCAAAAAATTGTAAAACTTTATGAACTCGAGGTAG
ATGAAGATGATGAGTGTGATGAAGAAAATTCAAATAATGCAAGTTTTGAAATAGAAATGA
AAATGTAAATCATTTATAATTTTGTTAGATGAAATTTCCTTTATTAACTTAATTCAGATG
TTGATTGAGATTTCTGCATTTAAGATTTATAATAAAGTGTGAGAATTAAATTATAATTGT
AGAAAAGGAAATGATAAAGACTTTGATGTAATTTTTTATTAAATATGCATGCTTGGTTGT
CCATTT
>g1972.t9 Gene=g1972 Length=691
MPIKILPPEEKIAVKSISWRMDERIIGIAYNNQLINLVDIESKEVIISYSVNADVTKICW
TQNSIDIDSNEKSILDDHVFLASLPSINSTISSGTKKSDYNSTRFYSNTGLNFLIVICND
CTIRAYIYGVLSCGSIDVKKKLNVNESDSLNIIEAKMSSNFERFFVVYVKNGILGTLVFE
NSALLKRHVALWKLSIKYGMILNIFEYMDDTIEHINEAWESVLLEMDNKLSKYAKKQEAG
SISADFLELLLFGYPSEELENFLTHEMTVRELKKLSNSVEMSYSTIQKLVVKPLHSAIIS
IFYHVNNLHGMHQNAYEYKNLLGENSSEALISTGSFLIKSHELQQIIDKSMRDFKIFFRW
LYIAISRLMDDTVPDDAGVITQQEVNYLAEFLYNFEENRKELVHDESGEKEIKFNLERVG
QYLTNQNLTIPSIDNTSNIWNEIFTQNECLQTSKLIYPHNKDSSLIQEKNKMEKSIKDLF
NRLEHSIGQEYNLKNDFIISHSDDIASSTIVTSHIIDGENQDAINLFTILLSEKDLLLLV
YYSNTYIPKIAKLQFTNRDECNILSVGQLSFIDIKFYNTRLLSGLIKNEIGNKIQTCFIQ
VPVSRLIDELLEYDQKTIPTFNMYNYIDDCNFKVIEGFAGNLMAVSGSRKVAAFLASNQK
IVKLYELEVDEDDECDEENSNNASFEIEMKM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g1972.t9 | PANTHER | PTHR13260 | ANAPHASE PROMOTING COMPLEX SUBUNIT 4 APC4 | 5 | 677 | 0e+00 |
| 2 | g1972.t9 | Pfam | PF12894 | Anaphase-promoting complex subunit 4 WD40 domain | 8 | 63 | 2e-07 |
| 1 | g1972.t9 | Pfam | PF12896 | Anaphase-promoting complex, cyclosome, subunit 4 | 181 | 371 | 0e+00 |
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:0031145 | anaphase-promoting complex-dependent catabolic process | BP |
| GO:0030071 | regulation of mitotic metaphase/anaphase transition | BP |
| GO:0005680 | anaphase-promoting complex | CC |
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.
