Gene loci information

Transcript annotation

  • This transcript has been annotated as Alpha-methylacyl-CoA racemase.

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 g15134 g15134.t1 TTS g15134.t1 4060216 4060216
chr_4 g15134 g15134.t1 isoform g15134.t1 4060285 4061544
chr_4 g15134 g15134.t1 exon g15134.t1.exon1 4060285 4060872
chr_4 g15134 g15134.t1 cds g15134.t1.CDS1 4060285 4060872
chr_4 g15134 g15134.t1 exon g15134.t1.exon2 4060931 4061377
chr_4 g15134 g15134.t1 cds g15134.t1.CDS2 4060931 4061377
chr_4 g15134 g15134.t1 exon g15134.t1.exon3 4061437 4061544
chr_4 g15134 g15134.t1 cds g15134.t1.CDS3 4061437 4061544
chr_4 g15134 g15134.t1 TSS g15134.t1 4061643 4061643

Sequences

>g15134.t1 Gene=g15134 Length=1143
ATGGCTCTAAAAGGACTAAAAGTTATTGAAATGGCAGGATTAGCTCCAGTTCCAATGTGT
GGAATGATTTTAGCTGATTTTGGAGCTCAAGTTACAAGAGTTGATAAAATTCCTTTACAT
CCATTTGACGTTCTTCAAGGTGGAAAACGAAATATTGCTCTAAACCTAAAAAAACCCAAA
GCTGTAGAAATAATGCGTAAAATGTGCAAAACATCAGATGTCATTATTGAACCATTTCGT
CCTGGTGTGATGGAAAAACTTGGACTTGGTCCAGAAGTGCTTTTGAAAGATAATCCAAAG
CTTATTTATGCACGTTTGACTGGCTTTGGTGCTGATGGTCGTGGAATTTATGCAAATCGT
GCAGGTCATGACATAAATTATATTGCGACTTCTGGTGTTCTTAGCATGTTTGGCAGAAAA
GGTGAAAAACCTTATGCACCAATAAATTTTGCAGCTGATTTTGCTGGTGGTGGAGTTTTA
TGTGCTTTTGGCATTTGTGTTGCACTTTTAGAAAGAAATCGATCAGGATTGGGTCAAATT
GTTGATAGTGCTATGGTTGATGGAAGTGCATACGTTGCAAGTTGGCTTTTTAGATCACGA
CATTTACCAGTTTGGTGTGGTGAAAGAGGTGAAAATACACTTGATGGTGGTGCACATTTC
TATGAAACTTATGAGACAAAAGATGGAAAATTTATGGCAGTTGGTGCAATTGAGCCACAA
TTTTATGCTGAATTATTAAAAGGCTTAGAACTCAGTGATGAAGAAATTGAATATAAAAAT
TTCGAAGAGAATAAAAAAATTTTTACTGAAATTTTCAAGAAAAAAACTCAAGCTGAATGG
TGTAAAATTTTTGATGGTGTTGATGCATGTGTGACACCAGTAATTCATTGGAATGAAGCA
AATGAGCATCCACATAATAAAGAAAGACAAGTTTTCAAAGATATTGATGGACTTCATGTA
CCAAATCCAGCACCAAAATTAAGTCGAACACCTGGTGTATCACAATTTGGTGTTGGTCAT
GATTCAGCCACTTTTGAAGTTGTTGAAGAAATTCTGAAAGAAATCGGAATTGAAAAAGAC
GAAATGAAAAATTTAATTGAAGAAAAAGTTTTGTGTATTGACGATGGAAAATCAAAATTA
TAA

>g15134.t1 Gene=g15134 Length=380
MALKGLKVIEMAGLAPVPMCGMILADFGAQVTRVDKIPLHPFDVLQGGKRNIALNLKKPK
AVEIMRKMCKTSDVIIEPFRPGVMEKLGLGPEVLLKDNPKLIYARLTGFGADGRGIYANR
AGHDINYIATSGVLSMFGRKGEKPYAPINFAADFAGGGVLCAFGICVALLERNRSGLGQI
VDSAMVDGSAYVASWLFRSRHLPVWCGERGENTLDGGAHFYETYETKDGKFMAVGAIEPQ
FYAELLKGLELSDEEIEYKNFEENKKIFTEIFKKKTQAEWCKIFDGVDACVTPVIHWNEA
NEHPHNKERQVFKDIDGLHVPNPAPKLSRTPGVSQFGVGHDSATFEVVEEILKEIGIEKD
EMKNLIEEKVLCIDDGKSKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g15134.t1 Coils Coil Coil 348 368 -
6 g15134.t1 Gene3D G3DSA:3.40.50.10540 - 3 313 2.7E-105
5 g15134.t1 Gene3D G3DSA:3.30.1540.10 - 211 295 2.7E-105
2 g15134.t1 PANTHER PTHR22923 CEREBELLIN-RELATED 1 377 5.4E-128
3 g15134.t1 PANTHER PTHR22923:SF101 ALPHA-METHYLACYL-COA RACEMASE 1 377 5.4E-128
1 g15134.t1 Pfam PF02515 CoA-transferase family III 3 333 1.0E-71
4 g15134.t1 SUPERFAMILY SSF89796 CoA-transferase family III (CaiB/BaiF) 2 371 7.59E-102

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:0008410 CoA-transferase activity MF

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