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.t3 isoform g13122.t3 28042939 28045158
chr_1 g13122 g13122.t3 exon g13122.t3.exon1 28042939 28043040
chr_1 g13122 g13122.t3 TSS g13122.t3 28042969 28042969
chr_1 g13122 g13122.t3 exon g13122.t3.exon2 28043146 28043403
chr_1 g13122 g13122.t3 cds g13122.t3.CDS1 28043207 28043403
chr_1 g13122 g13122.t3 exon g13122.t3.exon3 28043598 28043704
chr_1 g13122 g13122.t3 cds g13122.t3.CDS2 28043598 28043704
chr_1 g13122 g13122.t3 exon g13122.t3.exon4 28043772 28045001
chr_1 g13122 g13122.t3 cds g13122.t3.CDS3 28043772 28045001
chr_1 g13122 g13122.t3 exon g13122.t3.exon5 28045064 28045158
chr_1 g13122 g13122.t3 cds g13122.t3.CDS4 28045064 28045158
chr_1 g13122 g13122.t3 TTS g13122.t3 28045345 28045345

Sequences

>g13122.t3 Gene=g13122 Length=1792
AAAAGAATACGTAGAACGCCGGCATATGCTCATTCTATACGAAGTTGTTGAAGTGATCGG
TCTGCTGACGTTTCAGTTTCTTATTCTGTGAAGCATTTTAATTCAAAAGATCATTTACGT
CATTTATTTCTTGAGTTGAAAACAAAAAGAAGATAAAAAGAACATGTCTGAAACTAAGGA
AAAAATTGTTAATGGCACTTCTGCTGCGACAAAAAATGGTCAGCTTTGTCCATATAAAAT
ATTGAAAGATCTTCCTAAAGTTCTTCCATCGGATTTTATTTTGCCAAATTTGCCATCAAG
ATGTACATGGACAAGTGATAAGAACAAGCAAGCTGCATCACCTCATCCAAAAAGGACCTT
CAAAGAAAGACCAAAAGTTTGTGAAAATGTCTTGGAAGCAATTGGAATGACACCATTAGT
CAAATTGAATCACATTCCACAATCATTGGGTATCAAATGTCAAATGTATGCAAAGTGTGA
ATTCTTGAATCCAGGTGGTTCTGTCAAAGATAGAATTGGTTATCGCATGGTACTTGATGC
TGAAGAGAAAGGAATTTTGAAAGAAGGTTCAACAATTATTGAGCCAACATCAGGAAATAC
TGGTGTGGGCTTAGCTATGGCATGTGCTGTTCGTGGTTATCGCTGTATCATTGTTATGCC
CGAGAAAATGTCTGACGAAAAGGTCAACACTTTGAAAGCTCTCGGGGCAGAGATCATTCG
TACGCCAACTGAAGCCGCCTATGATAATCCCGATTCACTCATTGCTGTTGCACAGCGTTT
GCAAAAAGAAATTCCAAATTCATGGATTCCTGATCAATATCGCAATTGTGGTAATCCATT
GGCTCATTATGATGGAACTGGTGCTGAAATTTTGTATCAATTGGATGGCAAAGTTGATAT
GGTTGTGCTTGGAGCAGGAACAGGCGGAACAATTGCTGGTGTAGGTCGTCGAATTAAAGA
AGAATGTCCCAATTGTGTTATTGTTGGTGTTGACCCAGAAGGTTCAATTTTAGCACAACC
TGAATCACTCAATGAATCAAGTGTCACAATGTATGAAGTTGAAGGAATTGGTTACGATTT
TATTCCGACAGTACTTGATCGTTCAGTTGTTGATAAATGGTACAAATCAAACGACAAAAT
TTCACTTCCAATGGCAAGAAGACTGATTGCTGAAGAAGGATTCCTATGTGGTGGCTCAAG
TGGAGCAGCTATGTCTTGTGCAATTGCAGCTGCAAAGGATCTGACAGAAGATCAAACTTG
TGTTGTTATTTTGCCCGATAATATAAGAAATTATATGACAAAATTCGTCGTTGATAACTG
GCTAGAAGCAAGAGATTTGAAGAATTCTGTCAATACTCAAGATCATCCATGGTGGGATAA
TCAAGTTTCAAATTTGCACTTGCGTCCACCATTGACAGTCACAGAGAATGTTACATGCCA
AGAAGTGATCGATATTATGAAAAATGAAGATATTGATCAAATTCCAGTGATTGACAGCAA
TGGAAATGCAAAAGGGATGGCAACGATCAATTATCTCGTTAATCGCATGCTAAACTTCGG
TTTGAAATCATCAGACAAGATCGATAAAGCAGTTTTCAAGAAGTTCTCAAAAGTTGCATT
AGACACATCACTTGGTCGTCTTTCACGTATTTTGGAAAAAGATCCTTACGTGTTGGTTAC
TCAGAAACAAAAAGAATATGCAAATGGTGAAACTATTACAAGGGAAATTATTATCGGAAT
TATTACACAACGTGATTTGCTCAATTATGTTATGAAATTTCAACAAAAATAG

>g13122.t3 Gene=g13122 Length=542
MSETKEKIVNGTSAATKNGQLCPYKILKDLPKVLPSDFILPNLPSRCTWTSDKNKQAASP
HPKRTFKERPKVCENVLEAIGMTPLVKLNHIPQSLGIKCQMYAKCEFLNPGGSVKDRIGY
RMVLDAEEKGILKEGSTIIEPTSGNTGVGLAMACAVRGYRCIIVMPEKMSDEKVNTLKAL
GAEIIRTPTEAAYDNPDSLIAVAQRLQKEIPNSWIPDQYRNCGNPLAHYDGTGAEILYQL
DGKVDMVVLGAGTGGTIAGVGRRIKEECPNCVIVGVDPEGSILAQPESLNESSVTMYEVE
GIGYDFIPTVLDRSVVDKWYKSNDKISLPMARRLIAEEGFLCGGSSGAAMSCAIAAAKDL
TEDQTCVVILPDNIRNYMTKFVVDNWLEARDLKNSVNTQDHPWWDNQVSNLHLRPPLTVT
ENVTCQEVIDIMKNEDIDQIPVIDSNGNAKGMATINYLVNRMLNFGLKSSDKIDKAVFKK
FSKVALDTSLGRLSRILEKDPYVLVTQKQKEYANGETITREIIIGIITQRDLLNYVMKFQ
QK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13122.t3 CDD cd01561 CBS_like 81 379 8.64748E-133
9 g13122.t3 Gene3D G3DSA:3.40.50.1100 - 80 380 8.9E-129
8 g13122.t3 Gene3D G3DSA:3.40.50.1100 - 112 225 8.9E-129
7 g13122.t3 Gene3D G3DSA:3.10.580.10 - 393 542 7.4E-47
3 g13122.t3 PANTHER PTHR10314:SF177 CYSTATHIONINE BETA-SYNTHASE-RELATED 34 468 2.2E-189
4 g13122.t3 PANTHER PTHR10314 CYSTATHIONINE BETA-SYNTHASE 34 468 2.2E-189
2 g13122.t3 Pfam PF00291 Pyridoxal-phosphate dependent enzyme 78 372 8.5E-64
1 g13122.t3 Pfam PF00571 CBS domain 411 458 1.6E-6
11 g13122.t3 ProSitePatterns PS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. 104 122 -
15 g13122.t3 ProSiteProfiles PS51371 CBS domain profile. 412 469 10.969
16 g13122.t3 ProSiteProfiles PS51371 CBS domain profile. 473 542 5.7
12 g13122.t3 SMART SM00116 cbs_1 415 463 4.0E-6
13 g13122.t3 SMART SM00116 cbs_1 480 537 34.0
5 g13122.t3 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes 63 390 3.8E-97
6 g13122.t3 SUPERFAMILY SSF54631 CBS-domain pair 408 537 3.73E-15
14 g13122.t3 TIGRFAM TIGR01137 cysta_beta: cystathionine beta-synthase 74 537 2.1E-189

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