Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial.

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_3 g823 g823.t4 TTS g823.t4 6263611 6263611
chr_3 g823 g823.t4 isoform g823.t4 6263835 6265251
chr_3 g823 g823.t4 exon g823.t4.exon1 6263835 6263949
chr_3 g823 g823.t4 cds g823.t4.CDS1 6263835 6263949
chr_3 g823 g823.t4 exon g823.t4.exon2 6264350 6265251
chr_3 g823 g823.t4 cds g823.t4.CDS2 6264350 6265170
chr_3 g823 g823.t4 TSS g823.t4 NA NA

Sequences

>g823.t4 Gene=g823 Length=1017
CCTGTTGCAATTACATGTGGAAATACGAGCATCATTAAGCCATCTGAAAGAGATCCAGGT
GCAACACTTTTACTCTGTGAAATGCTCAATGAAGCAGGCTGTCCTCCAGGCGTTGTAAAC
GTTATTCATGGCGCTCACGATGCGGTCAATTTCATCTGTGATCATCCCGATATCAAGGCA
ATTTCATTCGTTGGTTCTGACCAGGCTGGCAAATACATTTACGAACGTGGTTGCCGCAAT
GGTAAACGTGTACAAAGCAACATGGGTGCAAAGAATCATGGTGTGGTAATGGCTGACGCA
AATAAGAATGCAACATTAAATCAACTCGCTGGTGCTGCATTTGGTGCTGCTGGTCAACGT
TGTATGGCATTGTCAACTGCAATCTTTGTTGGTGAAGCACGTGAATGGATTCCTGATTTG
GTTGAACGAGCTGCAAAATTAAAAGTTGGTCCAGGAGACAAACCCGGTGTTGATCTCGGT
CCAGTCATTTCACCACAATCAAAGAAACGTATTCTCGATCTTGTGCAGTCAGGCGTCGAT
GAAGGCGCGAAAATCGTCCTTGATGGACGTGACATTAAAATTGATGGCTATGAAAAGGGT
AACTTTGTTGGACCAACAATTCTCGTCAATGTGACGCCTTCAATGAAATGCTATAAAGAA
GAAATTTTCGGACCAGTTCTTGTATGTTTAACGGCAGAGACGCTTGATGAAGCCATTGAC
ATCATTAATAAGAACCCATACGGCAATGGCACAGCTATTTTCACAACGAATGGCGCGACA
GCGAGGAAATTTGTCAATGAAATTGATGTTGGACAAGTTGGCGTTAATGTTCCCATTCCT
GTGCCATTACCAATGTTCTCATTCACTGGATCACGTGGTAGTTTCTGGGGCTCAGAACAT
TTCTACGGTAAGCAAGGCATCAAGTTCTATACCCAAACGAAGACGGTTACTCAATTGTGG
CGCGAGACAGATGTGACGCATACTCAAGCAGCAGTTGCCATGCCCACAATGAAATAA

>g823.t4 Gene=g823 Length=311
MLNEAGCPPGVVNVIHGAHDAVNFICDHPDIKAISFVGSDQAGKYIYERGCRNGKRVQSN
MGAKNHGVVMADANKNATLNQLAGAAFGAAGQRCMALSTAIFVGEAREWIPDLVERAAKL
KVGPGDKPGVDLGPVISPQSKKRILDLVQSGVDEGAKIVLDGRDIKIDGYEKGNFVGPTI
LVNVTPSMKCYKEEIFGPVLVCLTAETLDEAIDIINKNPYGNGTAIFTTNGATARKFVNE
IDVGQVGVNVPIPVPLPMFSFTGSRGSFWGSEHFYGKQGIKFYTQTKTVTQLWRETDVTH
TQAAVAMPTMK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g823.t4 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A 1 62 1.7E-14
7 g823.t4 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A 64 296 1.1E-64
2 g823.t4 PANTHER PTHR43866:SF3 METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE [ACYLATING], MITOCHONDRIAL 2 310 7.6E-168
3 g823.t4 PANTHER PTHR43866 MALONATE-SEMIALDEHYDE DEHYDROGENASE 2 310 7.6E-168
1 g823.t4 Pfam PF00171 Aldehyde dehydrogenase family 2 289 4.5E-85
5 g823.t4 ProSitePatterns PS00070 Aldehyde dehydrogenases cysteine active site. 87 98 -
4 g823.t4 SUPERFAMILY SSF53720 ALDH-like 2 291 3.67E-86
8 g823.t4 TIGRFAM TIGR01722 MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating) 2 293 2.4E-150

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:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor MF
GO:0004491 methylmalonate-semialdehyde dehydrogenase (acylating) activity MF
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF

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