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.t1 TSS g13123.t1 28045997 28045997
chr_1 g13123 g13123.t1 isoform g13123.t1 28046065 28049438
chr_1 g13123 g13123.t1 exon g13123.t1.exon1 28046065 28046252
chr_1 g13123 g13123.t1 cds g13123.t1.CDS1 28046065 28046252
chr_1 g13123 g13123.t1 exon g13123.t1.exon2 28047860 28047966
chr_1 g13123 g13123.t1 cds g13123.t1.CDS2 28047860 28047966
chr_1 g13123 g13123.t1 exon g13123.t1.exon3 28048027 28049259
chr_1 g13123 g13123.t1 cds g13123.t1.CDS3 28048027 28049259
chr_1 g13123 g13123.t1 exon g13123.t1.exon4 28049320 28049438
chr_1 g13123 g13123.t1 cds g13123.t1.CDS4 28049320 28049438
chr_1 g13123 g13123.t1 TTS g13123.t1 28049656 28049656

Sequences

>g13123.t1 Gene=g13123 Length=1647
ATGTCTGAGAGTAAAGAAAGTGCAATGAATGGACATCAATCAACATGTTCAACACATTTG
AAGTACAAGGCACTTGATATGCCTGAAACTTTGCAACCTGACTTTGTTTATCCAGATGAA
CCATCAAAATGTACTTGGGTTCGCGATAAATCTAAACAAACTGCAACTCCACATACTGTA
AGACCTTTCCATGAAAGGCCAAAAACAATTCCTCATATTTTGGATGCAATCGGTATGACA
CCAATGGTAAAATTGAACAAAATCCCACAATCATTGGGCATTAAATGTCAAATGTACGCA
AAGTGTGAATTCTTGAATCCAGGTGGTTCTGTCAAAGATCGAATTGGTTATCGCATGGTA
CTTGATGCTGAAGAAAAAGGTTTACTCAAGCCAGGATATACAATTATTGAGCCAACATCA
GGAAATACAGGAATTGGCTTAGCTATGGCAAGTGCAGTTCGTGGTTATCGCTGCATTATC
GTTTTGCCTGAGAAAAATTCAGATGAAAAAGTCAATGCACTCAAGGCATTTGGAGCAGAA
ATAATTCGTACAAGAACTGAAGCTAAATTCGATGAGCCTGATTCATTAGTCGCTGTTGCT
CAACGCTTGCAGAAAGAAATTCCAAACTCTGTCATTTTAAATCAATACACAAATTGCGGC
AATCCATTGGCTCATTATGATGGAACTGGAAGTGAAATTTTGTATCAATTGGATGGAAAA
GTTGATATGGTCGTGCTTGGAGCAGGAACAGGCGGAACAATAACTGGTGTAGGTCGTCGA
ATTAAAGAAGAATGTCCCAATTGCAAAATTATTGGAGTTGACCCAGAAGGTTCAATTTTA
GCACAACCAGATTCTTTGAATAAAACGGATGTTGTGGTTTTTGATGTCGAAGGCATCGGT
TACGATTTTATTCCGACTGTTCTAGATCGCGATATTGTTGATAAATGGATCAAATCTAAT
GATAAGATGGCTTTTCCAATGGCAAAACGTCTAATTCGCGAAGAAGGCTTTTTATGTGGT
GGTTCATCTGGTGCAGCAATGGCAGCTGCAATCGAAGTCGCTAAAGATTTATCAGAAGAT
CAAGTTTGTGTTGTCATTTGTCCGGACAATATTCGTAATTACATGAGTAAATTTTTGGTT
GACAATTGGATGGAAGCAAGAGGTTTGAAAGAATCTGTTAATATTCATTGTCATCCTTGG
TGGGATAGTAAAATTTCAAACTTAATTGGAAATAATTCACCAATGACTGTTACTGAAAAT
GTTGCCTGCAAAGATATACTTGAGAAATTAAAGCAAAATCATTTGGAACAAGTTGCTGTA
ACTGATATACATGGTGGCATTAAAGGAATGGCAACTGTCAATCACATAATGTGCAAAATT
CTTGATCGTTCACTGAAATTTACTGATCCAATTTCAAAGGGATCATTTTCAAAGTTTATT
AAAATCAAAATAGACACAACTCTCGGACGATTGTCTAGAATTTTGGAGAAAGAAACTTTT
GTTGTTGTCGTTCAAAATCGCGAAACTTATGATAGCACTGAAACAAGAAATGTTGAGCAT
GTTATTGCAGTTCTTACCCAAAAAGATTTATTGAACCATTTGGCTAATTATCAATATTGC
AGTCATAATGGTGTCAATGGACATTAA

>g13123.t1 Gene=g13123 Length=548
MSESKESAMNGHQSTCSTHLKYKALDMPETLQPDFVYPDEPSKCTWVRDKSKQTATPHTV
RPFHERPKTIPHILDAIGMTPMVKLNKIPQSLGIKCQMYAKCEFLNPGGSVKDRIGYRMV
LDAEEKGLLKPGYTIIEPTSGNTGIGLAMASAVRGYRCIIVLPEKNSDEKVNALKAFGAE
IIRTRTEAKFDEPDSLVAVAQRLQKEIPNSVILNQYTNCGNPLAHYDGTGSEILYQLDGK
VDMVVLGAGTGGTITGVGRRIKEECPNCKIIGVDPEGSILAQPDSLNKTDVVVFDVEGIG
YDFIPTVLDRDIVDKWIKSNDKMAFPMAKRLIREEGFLCGGSSGAAMAAAIEVAKDLSED
QVCVVICPDNIRNYMSKFLVDNWMEARGLKESVNIHCHPWWDSKISNLIGNNSPMTVTEN
VACKDILEKLKQNHLEQVAVTDIHGGIKGMATVNHIMCKILDRSLKFTDPISKGSFSKFI
KIKIDTTLGRLSRILEKETFVVVVQNRETYDSTETRNVEHVIAVLTQKDLLNHLANYQYC
SHNGVNGH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13123.t1 CDD cd01561 CBS_like 78 376 4.20139E-122
8 g13123.t1 Gene3D G3DSA:3.40.50.1100 - 77 377 2.8E-129
7 g13123.t1 Gene3D G3DSA:3.40.50.1100 - 109 222 2.8E-129
6 g13123.t1 Gene3D G3DSA:3.10.580.10 - 390 539 2.8E-33
2 g13123.t1 PANTHER PTHR10314:SF177 CYSTATHIONINE BETA-SYNTHASE-RELATED 27 468 2.5E-186
3 g13123.t1 PANTHER PTHR10314 CYSTATHIONINE BETA-SYNTHASE 27 468 2.5E-186
1 g13123.t1 Pfam PF00291 Pyridoxal-phosphate dependent enzyme 75 367 1.4E-67
10 g13123.t1 ProSitePatterns PS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. 101 119 -
11 g13123.t1 SMART SM00116 cbs_1 413 461 1.4
12 g13123.t1 SMART SM00116 cbs_1 478 535 10.0
4 g13123.t1 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes 59 388 1.31E-98
5 g13123.t1 SUPERFAMILY SSF54631 CBS-domain pair 405 536 1.58E-9
13 g13123.t1 TIGRFAM TIGR01137 cysta_beta: cystathionine beta-synthase 71 535 1.3E-177

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:0019343 cysteine biosynthetic process via cystathionine BP
GO:0006535 cysteine biosynthetic process from serine BP
GO:0004122 cystathionine beta-synthase activity MF
GO:0005737 cytoplasm CC

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.

Raw TPM values