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 g13123 g13123.t2 TSS g13123.t2 28045997 28045997
chr_1 g13123 g13123.t2 isoform g13123.t2 28046065 28048434
chr_1 g13123 g13123.t2 exon g13123.t2.exon1 28046065 28046252
chr_1 g13123 g13123.t2 cds g13123.t2.CDS1 28046065 28046252
chr_1 g13123 g13123.t2 exon g13123.t2.exon2 28047860 28047966
chr_1 g13123 g13123.t2 cds g13123.t2.CDS2 28047860 28047966
chr_1 g13123 g13123.t2 exon g13123.t2.exon3 28048027 28048434
chr_1 g13123 g13123.t2 cds g13123.t2.CDS3 28048027 28048433
chr_1 g13123 g13123.t2 TTS g13123.t2 NA NA

Sequences

>g13123.t2 Gene=g13123 Length=703
ATGTCTGAGAGTAAAGAAAGTGCAATGAATGGACATCAATCAACATGTTCAACACATTTG
AAGTACAAGGCACTTGATATGCCTGAAACTTTGCAACCTGACTTTGTTTATCCAGATGAA
CCATCAAAATGTACTTGGGTTCGCGATAAATCTAAACAAACTGCAACTCCACATACTGTA
AGACCTTTCCATGAAAGGCCAAAAACAATTCCTCATATTTTGGATGCAATCGGTATGACA
CCAATGGTAAAATTGAACAAAATCCCACAATCATTGGGCATTAAATGTCAAATGTACGCA
AAGTGTGAATTCTTGAATCCAGGTGGTTCTGTCAAAGATCGAATTGGTTATCGCATGGTA
CTTGATGCTGAAGAAAAAGGTTTACTCAAGCCAGGATATACAATTATTGAGCCAACATCA
GGAAATACAGGAATTGGCTTAGCTATGGCAAGTGCAGTTCGTGGTTATCGCTGCATTATC
GTTTTGCCTGAGAAAAATTCAGATGAAAAAGTCAATGCACTCAAGGCATTTGGAGCAGAA
ATAATTCGTACAAGAACTGAAGCTAAATTCGATGAGCCTGATTCATTAGTCGCTGTTGCT
CAACGCTTGCAGAAAGAAATTCCAAACTCTGTCATTTTAAATCAATACACAAATTGCGGC
AATCCATTGGCTCATTATGATGGAACTGGAAGTGAAATTTTGT

>g13123.t2 Gene=g13123 Length=234
MSESKESAMNGHQSTCSTHLKYKALDMPETLQPDFVYPDEPSKCTWVRDKSKQTATPHTV
RPFHERPKTIPHILDAIGMTPMVKLNKIPQSLGIKCQMYAKCEFLNPGGSVKDRIGYRMV
LDAEEKGLLKPGYTIIEPTSGNTGIGLAMASAVRGYRCIIVLPEKNSDEKVNALKAFGAE
IIRTRTEAKFDEPDSLVAVAQRLQKEIPNSVILNQYTNCGNPLAHYDGTGSEIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g13123.t2 CDD cd01561 CBS_like 78 234 1.92792E-82
6 g13123.t2 Gene3D G3DSA:3.40.50.1100 - 106 228 5.6E-46
2 g13123.t2 PANTHER PTHR10314:SF177 CYSTATHIONINE BETA-SYNTHASE-RELATED 26 234 7.4E-94
3 g13123.t2 PANTHER PTHR10314 CYSTATHIONINE BETA-SYNTHASE 26 234 7.4E-94
1 g13123.t2 Pfam PF00291 Pyridoxal-phosphate dependent enzyme 74 234 6.1E-39
5 g13123.t2 ProSitePatterns PS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. 101 119 -
4 g13123.t2 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes 58 234 4.32E-55

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