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.t9 TTS g823.t9 6263611 6263611
chr_3 g823 g823.t9 isoform g823.t9 6263835 6270027
chr_3 g823 g823.t9 exon g823.t9.exon1 6263835 6263949
chr_3 g823 g823.t9 cds g823.t9.CDS1 6263835 6263949
chr_3 g823 g823.t9 exon g823.t9.exon2 6264350 6265255
chr_3 g823 g823.t9 cds g823.t9.CDS2 6264350 6265255
chr_3 g823 g823.t9 exon g823.t9.exon3 6265420 6265474
chr_3 g823 g823.t9 cds g823.t9.CDS3 6265420 6265474
chr_3 g823 g823.t9 exon g823.t9.exon4 6266159 6266192
chr_3 g823 g823.t9 cds g823.t9.CDS4 6266159 6266192
chr_3 g823 g823.t9 exon g823.t9.exon5 6266299 6266366
chr_3 g823 g823.t9 cds g823.t9.CDS5 6266299 6266366
chr_3 g823 g823.t9 exon g823.t9.exon6 6266441 6266801
chr_3 g823 g823.t9 cds g823.t9.CDS6 6266441 6266801
chr_3 g823 g823.t9 exon g823.t9.exon7 6268390 6268467
chr_3 g823 g823.t9 cds g823.t9.CDS7 6268390 6268419
chr_3 g823 g823.t9 exon g823.t9.exon8 6269925 6270027
chr_3 g823 g823.t9 TSS g823.t9 6270055 6270055

Sequences

>g823.t9 Gene=g823 Length=1720
GTGTACAAAAATTATCATCTAGAAACTTAATTTTAATTTAAAATTCAAATTGAATTTGTT
AAATTAATTTGTGAGAGTTGATAACAGCACTTGTTTATTGTGAATTAAAAATTTATCGTC
TTAAAAATAATCAACTGATAAAGAATTAATCATGTCGCTCTTCAGAATCGCATCAGCGGA
GGTACGCAATGTTATCAAGCGCTCATATAACACCACAAATGTCGCACCCACTGTCAAAAT
GTTCATTGATGGAAAATTTGTTGATTCACAAGCCAAAGAATGGATTGATTTACATGATCC
AGCAACAAATGAGCTTGTAACACGCGTTCCAAAGTGCACTCTTGATGAAATGAATGCTGC
TGTTGAATCATCGAAACGCGCTTTTAAGACATGGAGTCAAACATCAATTCTTACACGTCA
GCAAGTCATGCTCAAATTGCAGCATATTATTCGCGCCAATATGTCTGAATTAGCTAAGAA
TATTACAAAAGAACAGGGAAAAACACTTGTCGATGCTGAAGGCGATGTTTTAAGAGGATT
GCAGGTTGTTGAGCACATGTGCAGCATTACATCGCTTCAACAAGGCGAGACGATGCCAAA
TATTGCAAAGGATATGGATACTTATAGTTATACTCTTCCACTTGGAGTTACTGCTGGAAT
TACACCTTTCAATTTTCCTGCTATGATTCCACTTTGGATGTTCCCTGTTGCAATTACATG
TGGAAATACGAGCATCATTAAGCCATCTGAAAGAGATCCAGGTGCAACACTTTTACTCTG
TGAAATGCTCAATGAAGCAGGCTGTCCTCCAGGCGTTGTAAACGTTATTCATGGCGCTCA
CGATGCGGTCAATTTCATCTGTGATCATCCCGATATCAAGGCAATTTCATTCGTTGGTTC
TGACCAGGCTGGCAAATACATTTACGAACGTGGTTGCCGCAATGGTAAACGTGTACAAAG
CAACATGGGTGCAAAGAATCATGGTGTGGTAATGGCTGACGCAAATAAGAATGCAACATT
AAATCAACTCGCTGGTGCTGCATTTGGTGCTGCTGGTCAACGTTGTATGGCATTGTCAAC
TGCAATCTTTGTTGGTGAAGCACGTGAATGGATTCCTGATTTGGTTGAACGAGCTGCAAA
ATTAAAAGTTGGTCCAGGAGACAAACCCGGTGTTGATCTCGGTCCAGTCATTTCACCACA
ATCAAAGAAACGTATTCTCGATCTTGTGCAGTCAGGCGTCGATGAAGGCGCGAAAATCGT
CCTTGATGGACGTGACATTAAAATTGATGGCTATGAAAAGGGTAACTTTGTTGGACCAAC
AATTCTCGTCAATGTGACGCCTTCAATGAAATGCTATAAAGAAGAAATTTTCGGACCAGT
TCTTGTATGTTTAACGGCAGAGACGCTTGATGAAGCCATTGACATCATTAATAAGAACCC
ATACGGCAATGGCACAGCTATTTTCACAACGAATGGCGCGACAGCGAGGAAATTTGTCAA
TGAAATTGATGTTGGACAAGTTGGCGTTAATGTTCCCATTCCTGTGCCATTACCAATGTT
CTCATTCACTGGATCACGTGGTAGTTTCTGGGGCTCAGAACATTTCTACGGTAAGCAAGG
CATCAAGTTCTATACCCAAACGAAGACGGTTACTCAATTGTGGCGCGAGACAGATGTGAC
GCATACTCAAGCAGCAGTTGCCATGCCCACAATGAAATAA

>g823.t9 Gene=g823 Length=522
MSLFRIASAEVRNVIKRSYNTTNVAPTVKMFIDGKFVDSQAKEWIDLHDPATNELVTRVP
KCTLDEMNAAVESSKRAFKTWSQTSILTRQQVMLKLQHIIRANMSELAKNITKEQGKTLV
DAEGDVLRGLQVVEHMCSITSLQQGETMPNIAKDMDTYSYTLPLGVTAGITPFNFPAMIP
LWMFPVAITCGNTSIIKPSERDPGATLLLCEMLNEAGCPPGVVNVIHGAHDAVNFICDHP
DIKAISFVGSDQAGKYIYERGCRNGKRVQSNMGAKNHGVVMADANKNATLNQLAGAAFGA
AGQRCMALSTAIFVGEAREWIPDLVERAAKLKVGPGDKPGVDLGPVISPQSKKRILDLVQ
SGVDEGAKIVLDGRDIKIDGYEKGNFVGPTILVNVTPSMKCYKEEIFGPVLVCLTAETLD
EAIDIINKNPYGNGTAIFTTNGATARKFVNEIDVGQVGVNVPIPVPLPMFSFTGSRGSFW
GSEHFYGKQGIKFYTQTKTVTQLWRETDVTHTQAAVAMPTMK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g823.t9 CDD cd07085 ALDH_F6_MMSDH 28 504 0.0
6 g823.t9 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A 18 273 1.8E-77
7 g823.t9 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A 275 507 4.7E-64
2 g823.t9 PANTHER PTHR43866:SF3 METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE [ACYLATING], MITOCHONDRIAL 9 521 1.4E-276
3 g823.t9 PANTHER PTHR43866 MALONATE-SEMIALDEHYDE DEHYDROGENASE 9 521 1.4E-276
1 g823.t9 Pfam PF00171 Aldehyde dehydrogenase family 36 500 6.2E-137
5 g823.t9 ProSitePatterns PS00070 Aldehyde dehydrogenases cysteine active site. 298 309 -
4 g823.t9 SUPERFAMILY SSF53720 ALDH-like 18 502 3.53E-143
8 g823.t9 TIGRFAM TIGR01722 MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating) 28 504 3.0E-239

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

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