Gene loci information

Transcript annotation

  • This transcript has been annotated as Peroxisomal multifunctional enzyme type 2.

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_1 g12123 g12123.t2 isoform g12123.t2 21150759 21154467
chr_1 g12123 g12123.t2 exon g12123.t2.exon1 21150759 21150989
chr_1 g12123 g12123.t2 exon g12123.t2.exon2 21151266 21151566
chr_1 g12123 g12123.t2 cds g12123.t2.CDS1 21151279 21151566
chr_1 g12123 g12123.t2 exon g12123.t2.exon3 21151623 21151872
chr_1 g12123 g12123.t2 cds g12123.t2.CDS2 21151623 21151872
chr_1 g12123 g12123.t2 exon g12123.t2.exon4 21151944 21151985
chr_1 g12123 g12123.t2 cds g12123.t2.CDS3 21151944 21151985
chr_1 g12123 g12123.t2 exon g12123.t2.exon5 21152046 21152605
chr_1 g12123 g12123.t2 cds g12123.t2.CDS4 21152046 21152605
chr_1 g12123 g12123.t2 exon g12123.t2.exon6 21152703 21152826
chr_1 g12123 g12123.t2 cds g12123.t2.CDS5 21152703 21152826
chr_1 g12123 g12123.t2 exon g12123.t2.exon7 21152896 21153096
chr_1 g12123 g12123.t2 cds g12123.t2.CDS6 21152896 21153096
chr_1 g12123 g12123.t2 exon g12123.t2.exon8 21153157 21153426
chr_1 g12123 g12123.t2 cds g12123.t2.CDS7 21153157 21153426
chr_1 g12123 g12123.t2 exon g12123.t2.exon9 21153593 21153799
chr_1 g12123 g12123.t2 cds g12123.t2.CDS8 21153593 21153799
chr_1 g12123 g12123.t2 exon g12123.t2.exon10 21154256 21154467
chr_1 g12123 g12123.t2 cds g12123.t2.CDS9 21154256 21154467
chr_1 g12123 g12123.t2 TTS g12123.t2 21154817 21154817
chr_1 g12123 g12123.t2 TSS g12123.t2 NA NA

Sequences

>g12123.t2 Gene=g12123 Length=2398
ATCATTTTTCTTATATTCAATTAAATAACGAACACTTGTTCATAAAATATTCATTTTCAG
ACGGCGTTTACTTGCGGGGTATTCAATTGTGCTTTCGTATGTTTTTATTGTACATATATG
CTATAACACAGGCAGTCAGTCTTGTTGTTGTAGATATCTCGCGAAGAAATTTCACTTTTA
TATATTTTTGTTAAGAATATTTTTATTTTAGTTGTGAACTTGAAACGAAAGTCCTTCTGC
AATCATGGTTTTGAGATTTGACAATCGTGTTGTTGTTGTAACTGGTGCAGGTGCTGGTTT
AGGTAGAGAATATGCACTTTTATTTGGCAAGCGTGGTGCTAAAGTGGTTGTGAACGATCT
TGGTGGCAATTTTCATGGTGAAGGAAACTCATCTAGAGCTGCAGACTTGGTTGTAGAAGA
AATTAGAAAACTTGGAGGAACAGCAGTTGCTGATTACAATAGTGTCGTCGAAGGACATAA
AATTATTGAAACTGCAATTTCAAATTATGGACGCATTGATGTGCTTGTTAATAATGCCGG
AATTCTTCGTGATAAATCAATTGCCAACATCTCGGATAATGACTGGAATTTAATTCATGA
TGTTCACTTAAAGGGAAGCTTCATGACAACTCGTGCTGCTTGGCCATACTTTAAAAAACA
AAAGTTCGGTCGTATTATAATGACCACCAGTAATAGTGGAATTTATGGAAATTTCGGTCA
AGCTAACTATTCAGCAGCAAAGCTCGGTTTAATTGGATTAGCTAACACAGTTGCAATTGA
AGGTGCTAAATATAATGTTCATTGTAATACAATTTGTCCAACTGCTGCATCAAGAATGAC
AAAAGGTATTTTACCTGATGATCTATTTGATGAAATGAAACCAGAATTGATTGCACCAGT
AGTGGTTTACTTATGTCATGAAGACACAATGGATAATGGTCAAGTCATTGAGAGTGCAGT
TGGTTTTGCAACAAAAGTTCATTTTGTACGAGGCAAGGGAAGTTTAATTCGAGATAGCAT
CAAAGATGTTCCAACACCTGAAACTGTTAAGGCGAAATGGGGCAAAATTACTGACATGAA
GAATGCAAAGCATTTCAATTCAAATATGGAAGTCAGTTCTTCATTTGTCAGCGTTATGGA
TAGATTGAAAAATCCCTTGCCTAAAGATACATTTGAAGATACTTACACTTATACATTCCG
TGACACAATTCTATATGCATTGGGAATTGGAGTTGGAACCGAAGATGAAAGCAATTTGAA
ATTCATTTATGAAAATCATCCAAACTTTGCCGCATTCCCAACTTATGCAGTTATTCCTTC
TATTATTATGCTAATGACATCAAGCATAACACCATCAGCCCTGGAAAACTTTGATCTTTC
TCAAGTCTTGCATGGCGAACAATTTATTGAAATTGTAAATCCTATGAGAACAGAAGGAAC
ACTTACAACTCGTGGAAATGTGATTGATGTTCAACAGAAAAAATCTGGTGTTGTTGTTAC
TACTGAATGTCTTTCATATGATGAAGGCGGTCAACTTATGACACGATCACAGTCAAGTAC
ATTCATTGTACGCGGAAAATCAAACGGAAAATATGGTGGAAATCCAGAAAAAGTGATCAA
CATTATACCAAATCCAAGCAGACAACCTGATCACACTTCGATTGTCAAGACGAATGTTGA
TCAAGCTGCTTTATATCGTCTTTCAGGCGATCTCAATCCATTGCACATCGATCCAAATTT
TGCACTTCTTGGTGGTTTTAATCGTCCAATTATTCACGGTTTGTGCACTTTCGGTGTCTC
TGTTCGTGCAGTGTTGAAACAATATGCTGATAATGACCCATCACTTTTCAAGGCTGTTAA
AGTTCGTTTTACTAAACCTGTTTTTCCTGGTGATACCTTGAAAGTTGAGATGTGGCAAGA
AGGCAACAGAATTCATTTTAGAACTCTTCTCGCTGAGTCTAACACTGAAGTTATTAGTGG
CGCTTATGTGGATTTATTGAACGTTATAAAATCGACATCAACATCAGAAAGCATTCCACA
GTCATCTAGCAACATGGCACTTCAATCGGACGCAGTTTTTGCAGCAATTAAAGAACGAGT
CAATGCTGATAAAGCAAAGGCAAAAAGTGTTAATGGAGTTTTTCTTTATAAAATTACAAA
GGATGGAAAAGTTGCAAAAGAATGGACATTGGATTTGAAAAATGCAGTTATATCAGAAGG
TGCACCATCAGGAAAAGCCGATACAACAATCACTATTGCTGATGAAGACTTTATTGATAT
TGCCCTTGGTAAATTAAATCCACAACAAGCATTCATGAAGGGAAAACTAAAGATTCAGGG
AAATATTATGCTGGCACAAAAACTCAGCCCACTACTCAAGACAGATGCTAAATTGTAA

>g12123.t2 Gene=g12123 Length=717
MVLRFDNRVVVVTGAGAGLGREYALLFGKRGAKVVVNDLGGNFHGEGNSSRAADLVVEEI
RKLGGTAVADYNSVVEGHKIIETAISNYGRIDVLVNNAGILRDKSIANISDNDWNLIHDV
HLKGSFMTTRAAWPYFKKQKFGRIIMTTSNSGIYGNFGQANYSAAKLGLIGLANTVAIEG
AKYNVHCNTICPTAASRMTKGILPDDLFDEMKPELIAPVVVYLCHEDTMDNGQVIESAVG
FATKVHFVRGKGSLIRDSIKDVPTPETVKAKWGKITDMKNAKHFNSNMEVSSSFVSVMDR
LKNPLPKDTFEDTYTYTFRDTILYALGIGVGTEDESNLKFIYENHPNFAAFPTYAVIPSI
IMLMTSSITPSALENFDLSQVLHGEQFIEIVNPMRTEGTLTTRGNVIDVQQKKSGVVVTT
ECLSYDEGGQLMTRSQSSTFIVRGKSNGKYGGNPEKVINIIPNPSRQPDHTSIVKTNVDQ
AALYRLSGDLNPLHIDPNFALLGGFNRPIIHGLCTFGVSVRAVLKQYADNDPSLFKAVKV
RFTKPVFPGDTLKVEMWQEGNRIHFRTLLAESNTEVISGAYVDLLNVIKSTSTSESIPQS
SSNMALQSDAVFAAIKERVNADKAKAKSVNGVFLYKITKDGKVAKEWTLDLKNAVISEGA
PSGKADTTITIADEDFIDIALGKLNPQQAFMKGKLKIQGNIMLAQKLSPLLKTDAKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g12123.t2 CDD cd05353 hydroxyacyl-CoA-like_DH_SDR_c-like 3 252 1.18548E-155
20 g12123.t2 CDD cd03448 HDE_HSD 464 584 9.23385E-66
16 g12123.t2 Gene3D G3DSA:3.40.50.720 - 2 250 5.3E-72
19 g12123.t2 Gene3D G3DSA:3.30.160.260 - 251 304 5.0E-14
18 g12123.t2 Gene3D G3DSA:3.10.129.10 Hotdog Thioesterase 307 593 6.7E-91
17 g12123.t2 Gene3D G3DSA:3.30.1050.10 - 599 714 3.3E-42
4 g12123.t2 PANTHER PTHR45024 DEHYDROGENASES, SHORT CHAIN 2 303 9.9E-136
7 g12123.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 9 26 5.9E-21
6 g12123.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 89 100 2.1E-7
11 g12123.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 89 100 5.9E-21
9 g12123.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 136 152 5.9E-21
5 g12123.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 162 181 2.1E-7
10 g12123.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 162 181 5.9E-21
8 g12123.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 206 226 5.9E-21
2 g12123.t2 Pfam PF00106 short chain dehydrogenase 9 194 2.9E-39
3 g12123.t2 Pfam PF01575 MaoC like domain 464 578 2.5E-34
1 g12123.t2 Pfam PF02036 SCP-2 sterol transfer family 614 712 1.5E-24
22 g12123.t2 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 149 177 -
23 g12123.t2 SMART SM00822 This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group. 8 182 0.0031
12 g12123.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 245 6.57E-61
14 g12123.t2 SUPERFAMILY SSF54637 Thioesterase/thiol ester dehydrase-isomerase 311 449 1.85E-35
13 g12123.t2 SUPERFAMILY SSF54637 Thioesterase/thiol ester dehydrase-isomerase 464 581 1.64E-30
15 g12123.t2 SUPERFAMILY SSF55718 SCP-like 604 712 2.35E-35

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: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