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.t6 isoform g13123.t6 28048029 28049438
chr_1 g13123 g13123.t6 exon g13123.t6.exon1 28048029 28049259
chr_1 g13123 g13123.t6 cds g13123.t6.CDS1 28048086 28049259
chr_1 g13123 g13123.t6 exon g13123.t6.exon2 28049320 28049438
chr_1 g13123 g13123.t6 cds g13123.t6.CDS2 28049320 28049438
chr_1 g13123 g13123.t6 TTS g13123.t6 28049656 28049656
chr_1 g13123 g13123.t6 TSS g13123.t6 NA NA

Sequences

>g13123.t6 Gene=g13123 Length=1350
GCAAAGTGTGAATTCTTGAATCCAGGTGGTTCTGTCAAAGATCGAATTGGTTATCGCATG
GTACTTGATGCTGAAGAAAAAGGTTTACTCAAGCCAGGATATACAATTATTGAGCCAACA
TCAGGAAATACAGGAATTGGCTTAGCTATGGCAAGTGCAGTTCGTGGTTATCGCTGCATT
ATCGTTTTGCCTGAGAAAAATTCAGATGAAAAAGTCAATGCACTCAAGGCATTTGGAGCA
GAAATAATTCGTACAAGAACTGAAGCTAAATTCGATGAGCCTGATTCATTAGTCGCTGTT
GCTCAACGCTTGCAGAAAGAAATTCCAAACTCTGTCATTTTAAATCAATACACAAATTGC
GGCAATCCATTGGCTCATTATGATGGAACTGGAAGTGAAATTTTGTATCAATTGGATGGA
AAAGTTGATATGGTCGTGCTTGGAGCAGGAACAGGCGGAACAATAACTGGTGTAGGTCGT
CGAATTAAAGAAGAATGTCCCAATTGCAAAATTATTGGAGTTGACCCAGAAGGTTCAATT
TTAGCACAACCAGATTCTTTGAATAAAACGGATGTTGTGGTTTTTGATGTCGAAGGCATC
GGTTACGATTTTATTCCGACTGTTCTAGATCGCGATATTGTTGATAAATGGATCAAATCT
AATGATAAGATGGCTTTTCCAATGGCAAAACGTCTAATTCGCGAAGAAGGCTTTTTATGT
GGTGGTTCATCTGGTGCAGCAATGGCAGCTGCAATCGAAGTCGCTAAAGATTTATCAGAA
GATCAAGTTTGTGTTGTCATTTGTCCGGACAATATTCGTAATTACATGAGTAAATTTTTG
GTTGACAATTGGATGGAAGCAAGAGGTTTGAAAGAATCTGTTAATATTCATTGTCATCCT
TGGTGGGATAGTAAAATTTCAAACTTAATTGGAAATAATTCACCAATGACTGTTACTGAA
AATGTTGCCTGCAAAGATATACTTGAGAAATTAAAGCAAAATCATTTGGAACAAGTTGCT
GTAACTGATATACATGGTGGCATTAAAGGAATGGCAACTGTCAATCACATAATGTGCAAA
ATTCTTGATCGTTCACTGAAATTTACTGATCCAATTTCAAAGGGATCATTTTCAAAGTTT
ATTAAAATCAAAATAGACACAACTCTCGGACGATTGTCTAGAATTTTGGAGAAAGAAACT
TTTGTTGTTGTCGTTCAAAATCGCGAAACTTATGATAGCACTGAAACAAGAAATGTTGAG
CATGTTATTGCAGTTCTTACCCAAAAAGATTTATTGAACCATTTGGCTAATTATCAATAT
TGCAGTCATAATGGTGTCAATGGACATTAA

>g13123.t6 Gene=g13123 Length=430
MVLDAEEKGLLKPGYTIIEPTSGNTGIGLAMASAVRGYRCIIVLPEKNSDEKVNALKAFG
AEIIRTRTEAKFDEPDSLVAVAQRLQKEIPNSVILNQYTNCGNPLAHYDGTGSEILYQLD
GKVDMVVLGAGTGGTITGVGRRIKEECPNCKIIGVDPEGSILAQPDSLNKTDVVVFDVEG
IGYDFIPTVLDRDIVDKWIKSNDKMAFPMAKRLIREEGFLCGGSSGAAMAAAIEVAKDLS
EDQVCVVICPDNIRNYMSKFLVDNWMEARGLKESVNIHCHPWWDSKISNLIGNNSPMTVT
ENVACKDILEKLKQNHLEQVAVTDIHGGIKGMATVNHIMCKILDRSLKFTDPISKGSFSK
FIKIKIDTTLGRLSRILEKETFVVVVQNRETYDSTETRNVEHVIAVLTQKDLLNHLANYQ
YCSHNGVNGH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13123.t6 CDD cd01561 CBS_like 1 258 0.0
9 g13123.t6 Gene3D G3DSA:3.40.50.1100 - 1 104 0.0
10 g13123.t6 Gene3D G3DSA:3.40.50.1100 - 105 259 0.0
8 g13123.t6 Gene3D G3DSA:3.10.580.10 - 271 421 0.0
2 g13123.t6 PANTHER PTHR10314:SF177 CYSTATHIONINE BETA-SYNTHASE-RELATED 1 352 0.0
3 g13123.t6 PANTHER PTHR10314 CYSTATHIONINE BETA-SYNTHASE 1 352 0.0
1 g13123.t6 Pfam PF00291 Pyridoxal-phosphate dependent enzyme 1 249 0.0
6 g13123.t6 SMART SM00116 cbs_1 295 343 1.4
7 g13123.t6 SMART SM00116 cbs_1 360 417 10.0
4 g13123.t6 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes 1 270 0.0
5 g13123.t6 SUPERFAMILY SSF54631 CBS-domain pair 287 418 0.0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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