Gene loci information

Transcript annotation

  • This transcript has been annotated as Cystathionine beta-synthase.

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 g13122 g13122.t4 TSS g13122.t4 28042969 28042969
chr_1 g13122 g13122.t4 isoform g13122.t4 28043207 28044442
chr_1 g13122 g13122.t4 exon g13122.t4.exon1 28043207 28043403
chr_1 g13122 g13122.t4 cds g13122.t4.CDS1 28043207 28043403
chr_1 g13122 g13122.t4 exon g13122.t4.exon2 28043598 28043704
chr_1 g13122 g13122.t4 cds g13122.t4.CDS2 28043598 28043704
chr_1 g13122 g13122.t4 exon g13122.t4.exon3 28043772 28044442
chr_1 g13122 g13122.t4 cds g13122.t4.CDS3 28043772 28044442
chr_1 g13122 g13122.t4 TTS g13122.t4 28045345 28045345

Sequences

>g13122.t4 Gene=g13122 Length=975
ATGTCTGAAACTAAGGAAAAAATTGTTAATGGCACTTCTGCTGCGACAAAAAATGGTCAG
CTTTGTCCATATAAAATATTGAAAGATCTTCCTAAAGTTCTTCCATCGGATTTTATTTTG
CCAAATTTGCCATCAAGATGTACATGGACAAGTGATAAGAACAAGCAAGCTGCATCACCT
CATCCAAAAAGGACCTTCAAAGAAAGACCAAAAGTTTGTGAAAATGTCTTGGAAGCAATT
GGAATGACACCATTAGTCAAATTGAATCACATTCCACAATCATTGGGTATCAAATGTCAA
ATGTATGCAAAGTGTGAATTCTTGAATCCAGGTGGTTCTGTCAAAGATAGAATTGGTTAT
CGCATGGTACTTGATGCTGAAGAGAAAGGAATTTTGAAAGAAGGTTCAACAATTATTGAG
CCAACATCAGGAAATACTGGTGTGGGCTTAGCTATGGCATGTGCTGTTCGTGGTTATCGC
TGTATCATTGTTATGCCCGAGAAAATGTCTGACGAAAAGGTCAACACTTTGAAAGCTCTC
GGGGCAGAGATCATTCGTACGCCAACTGAAGCCGCCTATGATAATCCCGATTCACTCATT
GCTGTTGCACAGCGTTTGCAAAAAGAAATTCCAAATTCATGGATTCCTGATCAATATCGC
AATTGTGGTAATCCATTGGCTCATTATGATGGAACTGGTGCTGAAATTTTGTATCAATTG
GATGGCAAAGTTGATATGGTTGTGCTTGGAGCAGGAACAGGCGGAACAATTGCTGGTGTA
GGTCGTCGAATTAAAGAAGAATGTCCCAATTGTGTTATTGTTGGTGTTGACCCAGAAGGT
TCAATTTTAGCACAACCTGAATCACTCAATGAATCAAGTGTCACAATGTATGAAGTTGAA
GGAATTGGTTACGATTTTATTCCGACAGTACTTGATCGTTCAGTTGTTGATAAATGGTAC
AAATCAAACGACAAA

>g13122.t4 Gene=g13122 Length=325
MSETKEKIVNGTSAATKNGQLCPYKILKDLPKVLPSDFILPNLPSRCTWTSDKNKQAASP
HPKRTFKERPKVCENVLEAIGMTPLVKLNHIPQSLGIKCQMYAKCEFLNPGGSVKDRIGY
RMVLDAEEKGILKEGSTIIEPTSGNTGVGLAMACAVRGYRCIIVMPEKMSDEKVNTLKAL
GAEIIRTPTEAAYDNPDSLIAVAQRLQKEIPNSWIPDQYRNCGNPLAHYDGTGAEILYQL
DGKVDMVVLGAGTGGTIAGVGRRIKEECPNCVIVGVDPEGSILAQPESLNESSVTMYEVE
GIGYDFIPTVLDRSVVDKWYKSNDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13122.t4 CDD cd01561 CBS_like 81 325 1.79208E-115
7 g13122.t4 Gene3D G3DSA:3.40.50.1100 - 80 324 1.5E-107
6 g13122.t4 Gene3D G3DSA:3.40.50.1100 - 112 225 1.5E-107
2 g13122.t4 PANTHER PTHR10314:SF177 CYSTATHIONINE BETA-SYNTHASE-RELATED 34 325 7.9E-149
3 g13122.t4 PANTHER PTHR10314 CYSTATHIONINE BETA-SYNTHASE 34 325 7.9E-149
1 g13122.t4 Pfam PF00291 Pyridoxal-phosphate dependent enzyme 78 282 1.9E-55
5 g13122.t4 ProSitePatterns PS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. 104 122 -
4 g13122.t4 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes 63 324 5.76E-81

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:0006535 cysteine biosynthetic process from serine BP

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