General information for g13122.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cystathionine beta-synthase.
Parent gene
- The parent gene g13122 is located on chr_1: 28043777..28045158 (+ strand)
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.t1 | TSS | g13122.t1 | 28042969 | 28042969 |
| chr_1 | g13122 | g13122.t1 | isoform | g13122.t1 | 28043207 | 28045158 |
| chr_1 | g13122 | g13122.t1 | exon | g13122.t1.exon1 | 28043207 | 28043403 |
| chr_1 | g13122 | g13122.t1 | cds | g13122.t1.CDS1 | 28043207 | 28043403 |
| chr_1 | g13122 | g13122.t1 | exon | g13122.t1.exon2 | 28043598 | 28043704 |
| chr_1 | g13122 | g13122.t1 | cds | g13122.t1.CDS2 | 28043598 | 28043704 |
| chr_1 | g13122 | g13122.t1 | exon | g13122.t1.exon3 | 28043772 | 28045001 |
| chr_1 | g13122 | g13122.t1 | cds | g13122.t1.CDS3 | 28043772 | 28045001 |
| chr_1 | g13122 | g13122.t1 | exon | g13122.t1.exon4 | 28045064 | 28045158 |
| chr_1 | g13122 | g13122.t1 | cds | g13122.t1.CDS4 | 28045064 | 28045158 |
| chr_1 | g13122 | g13122.t1 | TTS | g13122.t1 | 28045345 | 28045345 |
Sequences
>g13122.t1 Gene=g13122 Length=1629
ATGTCTGAAACTAAGGAAAAAATTGTTAATGGCACTTCTGCTGCGACAAAAAATGGTCAG
CTTTGTCCATATAAAATATTGAAAGATCTTCCTAAAGTTCTTCCATCGGATTTTATTTTG
CCAAATTTGCCATCAAGATGTACATGGACAAGTGATAAGAACAAGCAAGCTGCATCACCT
CATCCAAAAAGGACCTTCAAAGAAAGACCAAAAGTTTGTGAAAATGTCTTGGAAGCAATT
GGAATGACACCATTAGTCAAATTGAATCACATTCCACAATCATTGGGTATCAAATGTCAA
ATGTATGCAAAGTGTGAATTCTTGAATCCAGGTGGTTCTGTCAAAGATAGAATTGGTTAT
CGCATGGTACTTGATGCTGAAGAGAAAGGAATTTTGAAAGAAGGTTCAACAATTATTGAG
CCAACATCAGGAAATACTGGTGTGGGCTTAGCTATGGCATGTGCTGTTCGTGGTTATCGC
TGTATCATTGTTATGCCCGAGAAAATGTCTGACGAAAAGGTCAACACTTTGAAAGCTCTC
GGGGCAGAGATCATTCGTACGCCAACTGAAGCCGCCTATGATAATCCCGATTCACTCATT
GCTGTTGCACAGCGTTTGCAAAAAGAAATTCCAAATTCATGGATTCCTGATCAATATCGC
AATTGTGGTAATCCATTGGCTCATTATGATGGAACTGGTGCTGAAATTTTGTATCAATTG
GATGGCAAAGTTGATATGGTTGTGCTTGGAGCAGGAACAGGCGGAACAATTGCTGGTGTA
GGTCGTCGAATTAAAGAAGAATGTCCCAATTGTGTTATTGTTGGTGTTGACCCAGAAGGT
TCAATTTTAGCACAACCTGAATCACTCAATGAATCAAGTGTCACAATGTATGAAGTTGAA
GGAATTGGTTACGATTTTATTCCGACAGTACTTGATCGTTCAGTTGTTGATAAATGGTAC
AAATCAAACGACAAAATTTCACTTCCAATGGCAAGAAGACTGATTGCTGAAGAAGGATTC
CTATGTGGTGGCTCAAGTGGAGCAGCTATGTCTTGTGCAATTGCAGCTGCAAAGGATCTG
ACAGAAGATCAAACTTGTGTTGTTATTTTGCCCGATAATATAAGAAATTATATGACAAAA
TTCGTCGTTGATAACTGGCTAGAAGCAAGAGATTTGAAGAATTCTGTCAATACTCAAGAT
CATCCATGGTGGGATAATCAAGTTTCAAATTTGCACTTGCGTCCACCATTGACAGTCACA
GAGAATGTTACATGCCAAGAAGTGATCGATATTATGAAAAATGAAGATATTGATCAAATT
CCAGTGATTGACAGCAATGGAAATGCAAAAGGGATGGCAACGATCAATTATCTCGTTAAT
CGCATGCTAAACTTCGGTTTGAAATCATCAGACAAGATCGATAAAGCAGTTTTCAAGAAG
TTCTCAAAAGTTGCATTAGACACATCACTTGGTCGTCTTTCACGTATTTTGGAAAAAGAT
CCTTACGTGTTGGTTACTCAGAAACAAAAAGAATATGCAAATGGTGAAACTATTACAAGG
GAAATTATTATCGGAATTATTACACAACGTGATTTGCTCAATTATGTTATGAAATTTCAA
CAAAAATAG
>g13122.t1 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.t1 | CDD | cd01561 | CBS_like | 81 | 379 | 8.64748E-133 |
| 9 | g13122.t1 | Gene3D | G3DSA:3.40.50.1100 | - | 80 | 380 | 8.9E-129 |
| 8 | g13122.t1 | Gene3D | G3DSA:3.40.50.1100 | - | 112 | 225 | 8.9E-129 |
| 7 | g13122.t1 | Gene3D | G3DSA:3.10.580.10 | - | 393 | 542 | 7.4E-47 |
| 3 | g13122.t1 | PANTHER | PTHR10314:SF177 | CYSTATHIONINE BETA-SYNTHASE-RELATED | 34 | 468 | 2.2E-189 |
| 4 | g13122.t1 | PANTHER | PTHR10314 | CYSTATHIONINE BETA-SYNTHASE | 34 | 468 | 2.2E-189 |
| 2 | g13122.t1 | Pfam | PF00291 | Pyridoxal-phosphate dependent enzyme | 78 | 372 | 8.5E-64 |
| 1 | g13122.t1 | Pfam | PF00571 | CBS domain | 411 | 458 | 1.6E-6 |
| 11 | g13122.t1 | ProSitePatterns | PS00901 | Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. | 104 | 122 | - |
| 15 | g13122.t1 | ProSiteProfiles | PS51371 | CBS domain profile. | 412 | 469 | 10.969 |
| 16 | g13122.t1 | ProSiteProfiles | PS51371 | CBS domain profile. | 473 | 542 | 5.7 |
| 12 | g13122.t1 | SMART | SM00116 | cbs_1 | 415 | 463 | 4.0E-6 |
| 13 | g13122.t1 | SMART | SM00116 | cbs_1 | 480 | 537 | 34.0 |
| 5 | g13122.t1 | SUPERFAMILY | SSF53686 | Tryptophan synthase beta subunit-like PLP-dependent enzymes | 63 | 390 | 3.8E-97 |
| 6 | g13122.t1 | SUPERFAMILY | SSF54631 | CBS-domain pair | 408 | 537 | 3.73E-15 |
| 14 | g13122.t1 | 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
- This transcript has been annotated with K01697 (cystathionine beta-synthase)
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.
