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.t5 TSS g12123.t5 21150894 21150894
chr_1 g12123 g12123.t5 isoform g12123.t5 21150983 21153797
chr_1 g12123 g12123.t5 exon g12123.t5.exon1 21150983 21150989
chr_1 g12123 g12123.t5 exon g12123.t5.exon2 21151266 21151566
chr_1 g12123 g12123.t5 cds g12123.t5.CDS1 21151279 21151566
chr_1 g12123 g12123.t5 exon g12123.t5.exon3 21151623 21151872
chr_1 g12123 g12123.t5 cds g12123.t5.CDS2 21151623 21151872
chr_1 g12123 g12123.t5 exon g12123.t5.exon4 21151944 21151985
chr_1 g12123 g12123.t5 cds g12123.t5.CDS3 21151944 21151985
chr_1 g12123 g12123.t5 exon g12123.t5.exon5 21152046 21152605
chr_1 g12123 g12123.t5 cds g12123.t5.CDS4 21152046 21152605
chr_1 g12123 g12123.t5 exon g12123.t5.exon6 21152703 21152826
chr_1 g12123 g12123.t5 cds g12123.t5.CDS5 21152703 21152826
chr_1 g12123 g12123.t5 exon g12123.t5.exon7 21152896 21153096
chr_1 g12123 g12123.t5 cds g12123.t5.CDS6 21152896 21153096
chr_1 g12123 g12123.t5 exon g12123.t5.exon8 21153157 21153426
chr_1 g12123 g12123.t5 cds g12123.t5.CDS7 21153157 21153426
chr_1 g12123 g12123.t5 exon g12123.t5.exon9 21153593 21153797
chr_1 g12123 g12123.t5 cds g12123.t5.CDS8 21153593 21153795
chr_1 g12123 g12123.t5 TTS g12123.t5 21154817 21154817

Sequences

>g12123.t5 Gene=g12123 Length=1960
ACGAAAGTCCTTCTGCAATCATGGTTTTGAGATTTGACAATCGTGTTGTTGTTGTAACTG
GTGCAGGTGCTGGTTTAGGTAGAGAATATGCACTTTTATTTGGCAAGCGTGGTGCTAAAG
TGGTTGTGAACGATCTTGGTGGCAATTTTCATGGTGAAGGAAACTCATCTAGAGCTGCAG
ACTTGGTTGTAGAAGAAATTAGAAAACTTGGAGGAACAGCAGTTGCTGATTACAATAGTG
TCGTCGAAGGACATAAAATTATTGAAACTGCAATTTCAAATTATGGACGCATTGATGTGC
TTGTTAATAATGCCGGAATTCTTCGTGATAAATCAATTGCCAACATCTCGGATAATGACT
GGAATTTAATTCATGATGTTCACTTAAAGGGAAGCTTCATGACAACTCGTGCTGCTTGGC
CATACTTTAAAAAACAAAAGTTCGGTCGTATTATAATGACCACCAGTAATAGTGGAATTT
ATGGAAATTTCGGTCAAGCTAACTATTCAGCAGCAAAGCTCGGTTTAATTGGATTAGCTA
ACACAGTTGCAATTGAAGGTGCTAAATATAATGTTCATTGTAATACAATTTGTCCAACTG
CTGCATCAAGAATGACAAAAGGTATTTTACCTGATGATCTATTTGATGAAATGAAACCAG
AATTGATTGCACCAGTAGTGGTTTACTTATGTCATGAAGACACAATGGATAATGGTCAAG
TCATTGAGAGTGCAGTTGGTTTTGCAACAAAAGTTCATTTTGTACGAGGCAAGGGAAGTT
TAATTCGAGATAGCATCAAAGATGTTCCAACACCTGAAACTGTTAAGGCGAAATGGGGCA
AAATTACTGACATGAAGAATGCAAAGCATTTCAATTCAAATATGGAAGTCAGTTCTTCAT
TTGTCAGCGTTATGGATAGATTGAAAAATCCCTTGCCTAAAGATACATTTGAAGATACTT
ACACTTATACATTCCGTGACACAATTCTATATGCATTGGGAATTGGAGTTGGAACCGAAG
ATGAAAGCAATTTGAAATTCATTTATGAAAATCATCCAAACTTTGCCGCATTCCCAACTT
ATGCAGTTATTCCTTCTATTATTATGCTAATGACATCAAGCATAACACCATCAGCCCTGG
AAAACTTTGATCTTTCTCAAGTCTTGCATGGCGAACAATTTATTGAAATTGTAAATCCTA
TGAGAACAGAAGGAACACTTACAACTCGTGGAAATGTGATTGATGTTCAACAGAAAAAAT
CTGGTGTTGTTGTTACTACTGAATGTCTTTCATATGATGAAGGCGGTCAACTTATGACAC
GATCACAGTCAAGTACATTCATTGTACGCGGAAAATCAAACGGAAAATATGGTGGAAATC
CAGAAAAAGTGATCAACATTATACCAAATCCAAGCAGACAACCTGATCACACTTCGATTG
TCAAGACGAATGTTGATCAAGCTGCTTTATATCGTCTTTCAGGCGATCTCAATCCATTGC
ACATCGATCCAAATTTTGCACTTCTTGGTGGTTTTAATCGTCCAATTATTCACGGTTTGT
GCACTTTCGGTGTCTCTGTTCGTGCAGTGTTGAAACAATATGCTGATAATGACCCATCAC
TTTTCAAGGCTGTTAAAGTTCGTTTTACTAAACCTGTTTTTCCTGGTGATACCTTGAAAG
TTGAGATGTGGCAAGAAGGCAACAGAATTCATTTTAGAACTCTTCTCGCTGAGTCTAACA
CTGAAGTTATTAGTGGCGCTTATGTGGATTTATTGAACGTTATAAAATCGACATCAACAT
CAGAAAGCATTCCACAGTCATCTAGCAACATGGCACTTCAATCGGACGCAGTTTTTGCAG
CAATTAAAGAACGAGTCAATGCTGATAAAGCAAAGGCAAAAAGTGTTAATGGAGTTTTTC
TTTATAAAATTACAAAGGATGGAAAAGTTGCAAAAGAATG

>g12123.t5 Gene=g12123 Length=646
MVLRFDNRVVVVTGAGAGLGREYALLFGKRGAKVVVNDLGGNFHGEGNSSRAADLVVEEI
RKLGGTAVADYNSVVEGHKIIETAISNYGRIDVLVNNAGILRDKSIANISDNDWNLIHDV
HLKGSFMTTRAAWPYFKKQKFGRIIMTTSNSGIYGNFGQANYSAAKLGLIGLANTVAIEG
AKYNVHCNTICPTAASRMTKGILPDDLFDEMKPELIAPVVVYLCHEDTMDNGQVIESAVG
FATKVHFVRGKGSLIRDSIKDVPTPETVKAKWGKITDMKNAKHFNSNMEVSSSFVSVMDR
LKNPLPKDTFEDTYTYTFRDTILYALGIGVGTEDESNLKFIYENHPNFAAFPTYAVIPSI
IMLMTSSITPSALENFDLSQVLHGEQFIEIVNPMRTEGTLTTRGNVIDVQQKKSGVVVTT
ECLSYDEGGQLMTRSQSSTFIVRGKSNGKYGGNPEKVINIIPNPSRQPDHTSIVKTNVDQ
AALYRLSGDLNPLHIDPNFALLGGFNRPIIHGLCTFGVSVRAVLKQYADNDPSLFKAVKV
RFTKPVFPGDTLKVEMWQEGNRIHFRTLLAESNTEVISGAYVDLLNVIKSTSTSESIPQS
SSNMALQSDAVFAAIKERVNADKAKAKSVNGVFLYKITKDGKVAKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g12123.t5 CDD cd05353 hydroxyacyl-CoA-like_DH_SDR_c-like 3 252 1.09274E-156
19 g12123.t5 CDD cd03448 HDE_HSD 464 584 2.79417E-66
15 g12123.t5 Gene3D G3DSA:3.40.50.720 - 2 250 4.3E-72
18 g12123.t5 Gene3D G3DSA:3.30.160.260 - 251 304 4.4E-14
17 g12123.t5 Gene3D G3DSA:3.10.129.10 Hotdog Thioesterase 307 593 5.3E-91
16 g12123.t5 Gene3D G3DSA:3.30.1050.10 - 599 646 1.3E-7
3 g12123.t5 PANTHER PTHR45024 DEHYDROGENASES, SHORT CHAIN 2 303 7.6E-136
6 g12123.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 9 26 3.7E-21
5 g12123.t5 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 89 100 1.7E-7
10 g12123.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 89 100 3.7E-21
8 g12123.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 136 152 3.7E-21
4 g12123.t5 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 162 181 1.7E-7
9 g12123.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 162 181 3.7E-21
7 g12123.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 206 226 3.7E-21
1 g12123.t5 Pfam PF00106 short chain dehydrogenase 9 194 2.4E-39
2 g12123.t5 Pfam PF01575 MaoC like domain 464 578 2.1E-34
21 g12123.t5 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 149 177 -
22 g12123.t5 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
11 g12123.t5 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 245 5.33E-61
13 g12123.t5 SUPERFAMILY SSF54637 Thioesterase/thiol ester dehydrase-isomerase 311 449 1.44E-35
12 g12123.t5 SUPERFAMILY SSF54637 Thioesterase/thiol ester dehydrase-isomerase 464 581 1.21E-30
14 g12123.t5 SUPERFAMILY SSF55718 SCP-like 604 643 5.89E-5

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