Gene loci information

Transcript annotation

  • This transcript has been annotated as Sarcosine dehydrogenase, 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_1 g11638 g11638.t4 TSS g11638.t4 17538070 17538070
chr_1 g11638 g11638.t4 isoform g11638.t4 17538144 17541915
chr_1 g11638 g11638.t4 exon g11638.t4.exon1 17538144 17538263
chr_1 g11638 g11638.t4 exon g11638.t4.exon2 17539196 17539323
chr_1 g11638 g11638.t4 exon g11638.t4.exon3 17539458 17539826
chr_1 g11638 g11638.t4 cds g11638.t4.CDS1 17539691 17539826
chr_1 g11638 g11638.t4 exon g11638.t4.exon4 17539906 17540094
chr_1 g11638 g11638.t4 cds g11638.t4.CDS2 17539906 17540094
chr_1 g11638 g11638.t4 exon g11638.t4.exon5 17540163 17540377
chr_1 g11638 g11638.t4 cds g11638.t4.CDS3 17540163 17540377
chr_1 g11638 g11638.t4 exon g11638.t4.exon6 17540603 17540669
chr_1 g11638 g11638.t4 cds g11638.t4.CDS4 17540603 17540669
chr_1 g11638 g11638.t4 exon g11638.t4.exon7 17540733 17540947
chr_1 g11638 g11638.t4 cds g11638.t4.CDS5 17540733 17540947
chr_1 g11638 g11638.t4 exon g11638.t4.exon8 17541148 17541327
chr_1 g11638 g11638.t4 cds g11638.t4.CDS6 17541148 17541327
chr_1 g11638 g11638.t4 exon g11638.t4.exon9 17541393 17541535
chr_1 g11638 g11638.t4 cds g11638.t4.CDS7 17541393 17541535
chr_1 g11638 g11638.t4 exon g11638.t4.exon10 17541596 17541708
chr_1 g11638 g11638.t4 cds g11638.t4.CDS8 17541596 17541708
chr_1 g11638 g11638.t4 exon g11638.t4.exon11 17541784 17541915
chr_1 g11638 g11638.t4 cds g11638.t4.CDS9 17541784 17541914
chr_1 g11638 g11638.t4 TTS g11638.t4 NA NA

Sequences

>g11638.t4 Gene=g11638 Length=1871
ATGTTACGTTTTAAAAGGAAATTTATTGATTGCATCAAGATACAAAGGAAGCAATTTGTT
CGATGTTTTTCAACTCCAACTTCATTGCCTGAATATGCTGACGTTGTTATAATAGGTGAT
GTGGTGGTGTTGCTGGATGCAGTACACTTTATCAATTAACTAAGCGTAATGTAAATGCAG
TGTTATTAGAACGCGGTCAACTAACATGTGGTACTACATGGCATACCGGCAAGTTATTAA
GTTTATCTAATCTGAAACTGGGTTGAACAGCGGTTGGATCAACAATGGCGGTTTATTCAT
CTCGCATTCACCGCAGCGCACAAATGAATATCGACGACTACAAACGCTTGGAAAAAGTTT
TGGTATCGAAAGTCGAATTCTGTCACCCCTTGAAGTTCAAAAAGAAGTTTTCCCATTGCT
CGATCCGAAATCGTTTGAAAATGCTTTATTCTCACCGGGTGATGGAGTAGTTGATCCAGC
AATGCTTTGCACAGCTCTTACACGTGCTGCAACATCAAACGGTGGTAGAGTATTTGAAAA
TTGTGCGGTTGACGAGTTGATTGTGGGTAAAACATTCCTCGGAGACAGGGAAATAAGAGG
TGTTAAAACACAAAATGGTATAATAAAGACAAATACAGTTGTAAATGCAACAGGAGTGTG
GGGAAAAGATTTATTGGAGCCGTTAGATATACATTTACCTCTTGTGCCGATGCGTCATGC
TTATGTCGTTTCTGAGGCGATCAAAGAAGTGCAGGGAATGCCAAATGTTCGCGATCACGA
CTACAGTCTCTATTTCCGTATTCAAGGTCAATCTATACAAATGGGAGGTTATGAAAATAA
TCCGATTTTACTTGACAAAGTTCCAGCTGATTTTCAATTTGGGCTTTATGATTTAGATTA
TTCAGTTTTTGACACACACATTGAAGGCGCAGTGAAACTTTGTCCGACATTCGGTCAAGC
AGGTATAAAAAGTACTATTTGTGGCCCAGAAAGCTTCACGCCTGATCATAAGCCTCTAAT
GGGCCCAGATCCAATTCTTTCTGGATTATTTCATAGCTGTGGATACAATAGTGCTGGCAT
GATGTTAAGTTGTGCAAAGCAATTAGCTTCATGGATTATACATGATAGACCAGATTTGCA
TTTATTTGCCTATGATATTAGAAGATTTACACCGAGACAAAGGAAAGCATATACTTGGGC
TATAGAAAGAAGTCATGAAGCCTACGCAAAAAATTATAGCATTGTCTTTCCAAATGACCA
GCCGCTTGCAGGAAGAAATTTTATTCAAGATCCATTCCATAAATTTCTTGTTGTTTTATT
ACAAGGATTTGAGCGACCTGGCTATTACATTCATGATGGTATAGCTCCCGTTCAGAAATA
CGATTATTATGGCTATTATGGTCGCGAGAAAAATAAGAATACTTGCTATGCTGAGAAACT
TGCTGGTGATTATAAATTTGAGTTTTCAGACCATCATGATCTTATTAGTGAAGAAGCTCA
TTCGTGTCGAGAAAATGCAGTGGTATTTAATTTGAGTTATTTTTGTAAAGTATTCATTAC
TGGTTCACAAGCTGAAGAAGCAGCAAAATGGATTTTCACAGCAGATCTAAATAAGCCATT
TAATAAAACGATCTATACGTGTGCATTAAATAACCGTGGTGGTGTCGAAATTGATTTGAC
AGTTACAGGAATAGAATCTGGTGTTGGTGAACTTCATGATCCTATATTTAAGGGCCGTGG
ATATTATGCTGTTTGTGGTGGAGCTTCTTCCTATCATTCCATAGCACACATGCAAGAGGC
GATTCGTGAGAAAGGTTTCCGCGCTAAACTCTGTGATGTAACACATGAACTTGGCATTCT
ATCATTACAAG

>g11638.t4 Gene=g11638 Length=463
MLCTALTRAATSNGGRVFENCAVDELIVGKTFLGDREIRGVKTQNGIIKTNTVVNATGVW
GKDLLEPLDIHLPLVPMRHAYVVSEAIKEVQGMPNVRDHDYSLYFRIQGQSIQMGGYENN
PILLDKVPADFQFGLYDLDYSVFDTHIEGAVKLCPTFGQAGIKSTICGPESFTPDHKPLM
GPDPILSGLFHSCGYNSAGMMLSCAKQLASWIIHDRPDLHLFAYDIRRFTPRQRKAYTWA
IERSHEAYAKNYSIVFPNDQPLAGRNFIQDPFHKFLVVLLQGFERPGYYIHDGIAPVQKY
DYYGYYGREKNKNTCYAEKLAGDYKFEFSDHHDLISEEAHSCRENAVVFNLSYFCKVFIT
GSQAEEAAKWIFTADLNKPFNKTIYTCALNNRGGVEIDLTVTGIESGVGELHDPIFKGRG
YYAVCGGASSYHSIAHMQEAIREKGFRAKLCDVTHELGILSLQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11638.t4 Gene3D G3DSA:3.50.50.60 - 1 97 0
10 g11638.t4 Gene3D G3DSA:3.50.50.60 - 159 258 0
9 g11638.t4 Gene3D G3DSA:3.30.1360.120 Probable tRNA modification gtpase trme; domain 1 308 463 0
4 g11638.t4 PANTHER PTHR13847 SARCOSINE DEHYDROGENASE-RELATED 1 339 0
5 g11638.t4 PANTHER PTHR13847:SF200 SARCOSINE DEHYDROGENASE, MITOCHONDRIAL 1 339 0
2 g11638.t4 Pfam PF01266 FAD dependent oxidoreductase 2 205 0
1 g11638.t4 Pfam PF16350 FAD dependent oxidoreductase central domain 215 267 0
3 g11638.t4 Pfam PF01571 Aminomethyltransferase folate-binding domain 281 463 0
8 g11638.t4 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain 2 252 0
7 g11638.t4 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain 74 173 0
6 g11638.t4 SUPERFAMILY SSF103025 Folate-binding domain 278 463 0

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:0005515 protein binding 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