Gene loci information

Transcript annotation

  • This transcript has been annotated as Gamma-butyrobetaine dioxygenase.

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 g10710 g10710.t1 TTS g10710.t1 11492574 11492574
chr_1 g10710 g10710.t1 isoform g10710.t1 11492642 11493969
chr_1 g10710 g10710.t1 exon g10710.t1.exon1 11492642 11493721
chr_1 g10710 g10710.t1 cds g10710.t1.CDS1 11492642 11493721
chr_1 g10710 g10710.t1 exon g10710.t1.exon2 11493784 11493969
chr_1 g10710 g10710.t1 cds g10710.t1.CDS2 11493784 11493969
chr_1 g10710 g10710.t1 TSS g10710.t1 11494022 11494022

Sequences

>g10710.t1 Gene=g10710 Length=1266
ATGTTTCGATATGTGCTTAAAAACTATATGAATAATAACAACAATCGTGTCTTAATTATT
CGTCATTTTAGTTCAGTAAATGCAAATGCTAATTTCAATGATAAAACTATAGAATTGCAT
ATTACAAAAAATAACACAACTACAAAACATTCATTTCCATTCGTATGGCTTCGTGATAAT
TGTAAATGTGATGCTTGCTTACATAAAGCTTCATCAAGTCGAATAATTAATTGGGAACAA
TTTGATCTAAATGTGAAGCCAAAAAGTGTTGAATATCATAATGAAAGGAAAATTTTAAAA
ATTAAATGGAATGATAAAGATGAACACATATCAGAATTTTCATATGAATGGCTTGAAGCG
AGAAATTTCAGCAAAAGCAATCGTGAAGAATATTTGAAAAAATTTTATTGTCTTCCAAAG
AAATTGTGGGGTAAAAATGAATATAGCAGTGCAATGGAATATTTTGATTTTACAAAAATC
CTTGAAAGCGATCTTGAACTTTATAAATGGTTGAAAAGTTTTTCAATTAATGGAATTGCA
ACAATAACTGGAGTTTCATCGACTGAAAATGAAGTACGTAAAATTGCTGATCGAGTTGGA
TTTATAAGGAAAACTCATTATGGTGAAGAATTTATGGTAAAGGCGAAAGATAATACTTCA
AATGTAGCTTATTTATCATCTAATCTTCAAATGCACACTGATTTGCCTTACTATGAATAT
GTACCCGGTGTTAATCTTCTTCATTGTTTGGTTCAATCAAAATCTGATGGTGCACAAAAT
CTTCTTGTTGATGGTTTTTACATTGCTGAAAAATTAAGAAAAGAATATCCAAAAGAGTTC
AAATTGCTGACTACAGTTTTAATTGATTGGTCAGATATTGGACAGGAGGATGAGAAATCA
TTTCATTCAATATATCGTGCTCCAATGATTTGTACAGATTATGATGGCAGATTGACACGA
ATAAATCATAGCATACCACAACGTGATTCTTTTTTTGCAGTTCCTATTGAAGAAGTTCAA
GAATGGTATAAAGCATTGTCACTATTCATAAAATTAATTTATGATGAAGCAATAGAACTT
AAAACAAAGGAAGGTACAATCTTATGCTTTGATAATCGAAGAGCGGTTCATGGAAGAAAA
CAATACATAGATACAGATGATAATTGTAGACATATTATTGGTGCTTATTTAGATTGGGAT
GAAATTTATTCTAAACTTCGAGTTTTACAGAAAAAATATGATGAAAATTTTAAATATGTA
ATTTAA

>g10710.t1 Gene=g10710 Length=421
MFRYVLKNYMNNNNNRVLIIRHFSSVNANANFNDKTIELHITKNNTTTKHSFPFVWLRDN
CKCDACLHKASSSRIINWEQFDLNVKPKSVEYHNERKILKIKWNDKDEHISEFSYEWLEA
RNFSKSNREEYLKKFYCLPKKLWGKNEYSSAMEYFDFTKILESDLELYKWLKSFSINGIA
TITGVSSTENEVRKIADRVGFIRKTHYGEEFMVKAKDNTSNVAYLSSNLQMHTDLPYYEY
VPGVNLLHCLVQSKSDGAQNLLVDGFYIAEKLRKEYPKEFKLLTTVLIDWSDIGQEDEKS
FHSIYRAPMICTDYDGRLTRINHSIPQRDSFFAVPIEEVQEWYKALSLFIKLIYDEAIEL
KTKEGTILCFDNRRAVHGRKQYIDTDDNCRHIIGAYLDWDEIYSKLRVLQKKYDENFKYV
I

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10710.t1 CDD cd00250 CAS_like 134 400 0
7 g10710.t1 Gene3D G3DSA:3.30.2020.30 - 24 124 0
6 g10710.t1 Gene3D G3DSA:3.60.130.10 - 125 416 0
3 g10710.t1 PANTHER PTHR10696 GAMMA-BUTYROBETAINE HYDROXYLASE-RELATED 47 411 0
4 g10710.t1 PANTHER PTHR10696:SF33 GAMMA-BUTYROBETAINE DIOXYGENASE 47 411 0
1 g10710.t1 Pfam PF06155 Gamma-butyrobetaine hydroxylase-like, N-terminal 39 118 0
2 g10710.t1 Pfam PF02668 Taurine catabolism dioxygenase TauD, TfdA family 154 396 0
5 g10710.t1 SUPERFAMILY SSF51197 Clavaminate synthase-like 107 414 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: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