Gene loci information

Transcript annotation

  • This transcript has been annotated as Trimethyllysine dioxygenase, 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 g9545 g9545.t1 TTS g9545.t1 4018831 4018831
chr_1 g9545 g9545.t1 isoform g9545.t1 4018903 4020047
chr_1 g9545 g9545.t1 exon g9545.t1.exon1 4018903 4019447
chr_1 g9545 g9545.t1 cds g9545.t1.CDS1 4018903 4019447
chr_1 g9545 g9545.t1 exon g9545.t1.exon2 4019510 4020047
chr_1 g9545 g9545.t1 cds g9545.t1.CDS2 4019510 4020047
chr_1 g9545 g9545.t1 TSS g9545.t1 4020151 4020151

Sequences

>g9545.t1 Gene=g9545 Length=1083
ATGTCAAAGTTTGAAACAATTAAAATTAAATTTCATGAAAATCTTTATGAAATTGACACG
TTTTGGTTACGAGATCATTGCCGATGCGTTCATTGTTACAATATTGAAACTTTCCAACGT
AAGACTAATATTTTGGATATACCAGATGATATCAATGCAAGTGATTTTATAATAAAGAAC
GGAAAACTACAAGTTTTCTGGAATGACGGACACGAATCTTCATATGACCTTGATTTCATA
TTGAAAAATCTTAATCCGCAATCTGATAAATACAAAAGAGTTTATTGGACTAAAGAAACA
TTTAAAGTGCTTGAAAAAGTTGAAATGAGCGATTTTCTTACCAATTCTGATACAAAATTG
GCAGTTTTGAAAAACCTTTACCTTTATGGGTTTGCATTTATCGATGGAGTTGAACCAACT
GAAGAAGGAACAAAGCAGTGCATTGAAAATCTTTTTCAAATTCAAAAAACTTTCTTTGGA
GAAATGTGGACATTTTCTGATGCAAATTTAGATCATTGCGATACAGCATATACAAATTAT
TATCTCCCAGGTCATAATGACAACACTTACTTCAATGATCCTGCTGGCTTGCAAATTTTA
CACTGTGTGCAAGATAATTGTACTGGTGGTGAAAATTTTTTAATTGATGGCTATCAAGTT
GCTACAAAAATTAAGAAAAATTATCCTGAAATTTACAAACGACTTACAACAACACTTGTG
CCAGCAGAATTCATTGAAAATGATCGTCATCATTCTTATTGTGCTCCAATTTTTCAACTT
CATCCATTGACTAAAGAAATTCTTCAAATTCGTTTCAATGATTCCGATCGAGCACCATTT
AATACTTTGAAACAAACAGAAGTTCGTCAATTTTATAAAGATTTAAAGTTTTTGGCAAAT
GAATTCAACCACGATGAAAATCAAATTGTTTTCAAGTTAAAGCCAGGTAGAGTTATGATT
TTTGACAATTGGAGAGTTCTTCATGGTCGCTATAGTTATGATGGATGTCGTACAATGAGT
GGCAGTTATGTTTCAAGGACTGAATTTCAGTCAGTGTTGCGTGTCAATGGTTTGATAAAT
TGA

>g9545.t1 Gene=g9545 Length=360
MSKFETIKIKFHENLYEIDTFWLRDHCRCVHCYNIETFQRKTNILDIPDDINASDFIIKN
GKLQVFWNDGHESSYDLDFILKNLNPQSDKYKRVYWTKETFKVLEKVEMSDFLTNSDTKL
AVLKNLYLYGFAFIDGVEPTEEGTKQCIENLFQIQKTFFGEMWTFSDANLDHCDTAYTNY
YLPGHNDNTYFNDPAGLQILHCVQDNCTGGENFLIDGYQVATKIKKNYPEIYKRLTTTLV
PAEFIENDRHHSYCAPIFQLHPLTKEILQIRFNDSDRAPFNTLKQTEVRQFYKDLKFLAN
EFNHDENQIVFKLKPGRVMIFDNWRVLHGRYSYDGCRTMSGSYVSRTEFQSVLRVNGLIN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9545.t1 Gene3D G3DSA:3.30.2020.30 - 1 83 0
6 g9545.t1 Gene3D G3DSA:3.60.130.10 - 84 357 0
3 g9545.t1 PANTHER PTHR10696:SF3 TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL 18 356 0
4 g9545.t1 PANTHER PTHR10696 GAMMA-BUTYROBETAINE HYDROXYLASE-RELATED 18 356 0
1 g9545.t1 Pfam PF06155 Gamma-butyrobetaine hydroxylase-like, N-terminal 6 79 0
2 g9545.t1 Pfam PF02668 Taurine catabolism dioxygenase TauD, TfdA family 106 343 0
5 g9545.t1 SUPERFAMILY SSF51197 Clavaminate synthase-like 65 355 0
8 g9545.t1 TIGRFAM TIGR02410 carnitine_TMLD: trimethyllysine dioxygenase 19 354 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:0050353 trimethyllysine dioxygenase activity MF
GO:0005506 iron ion binding MF
GO:0045329 carnitine biosynthetic process BP
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF

KEGG

Orthology

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. There were no conditions that were differentially expressed