General information for g13122.t6
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.t6 | TSS | g13122.t6 | 28042969 | 28042969 |
| chr_1 | g13122 | g13122.t6 | isoform | g13122.t6 | 28043777 | 28045158 |
| chr_1 | g13122 | g13122.t6 | exon | g13122.t6.exon1 | 28043777 | 28045001 |
| chr_1 | g13122 | g13122.t6 | cds | g13122.t6.CDS1 | 28043831 | 28045001 |
| chr_1 | g13122 | g13122.t6 | exon | g13122.t6.exon2 | 28045064 | 28045158 |
| chr_1 | g13122 | g13122.t6 | cds | g13122.t6.CDS2 | 28045064 | 28045158 |
| chr_1 | g13122 | g13122.t6 | TTS | g13122.t6 | 28045345 | 28045345 |
Sequences
>g13122.t6 Gene=g13122 Length=1320
AAGTGTGAATTCTTGAATCCAGGTGGTTCTGTCAAAGATAGAATTGGTTATCGCATGGTA
CTTGATGCTGAAGAGAAAGGAATTTTGAAAGAAGGTTCAACAATTATTGAGCCAACATCA
GGAAATACTGGTGTGGGCTTAGCTATGGCATGTGCTGTTCGTGGTTATCGCTGTATCATT
GTTATGCCCGAGAAAATGTCTGACGAAAAGGTCAACACTTTGAAAGCTCTCGGGGCAGAG
ATCATTCGTACGCCAACTGAAGCCGCCTATGATAATCCCGATTCACTCATTGCTGTTGCA
CAGCGTTTGCAAAAAGAAATTCCAAATTCATGGATTCCTGATCAATATCGCAATTGTGGT
AATCCATTGGCTCATTATGATGGAACTGGTGCTGAAATTTTGTATCAATTGGATGGCAAA
GTTGATATGGTTGTGCTTGGAGCAGGAACAGGCGGAACAATTGCTGGTGTAGGTCGTCGA
ATTAAAGAAGAATGTCCCAATTGTGTTATTGTTGGTGTTGACCCAGAAGGTTCAATTTTA
GCACAACCTGAATCACTCAATGAATCAAGTGTCACAATGTATGAAGTTGAAGGAATTGGT
TACGATTTTATTCCGACAGTACTTGATCGTTCAGTTGTTGATAAATGGTACAAATCAAAC
GACAAAATTTCACTTCCAATGGCAAGAAGACTGATTGCTGAAGAAGGATTCCTATGTGGT
GGCTCAAGTGGAGCAGCTATGTCTTGTGCAATTGCAGCTGCAAAGGATCTGACAGAAGAT
CAAACTTGTGTTGTTATTTTGCCCGATAATATAAGAAATTATATGACAAAATTCGTCGTT
GATAACTGGCTAGAAGCAAGAGATTTGAAGAATTCTGTCAATACTCAAGATCATCCATGG
TGGGATAATCAAGTTTCAAATTTGCACTTGCGTCCACCATTGACAGTCACAGAGAATGTT
ACATGCCAAGAAGTGATCGATATTATGAAAAATGAAGATATTGATCAAATTCCAGTGATT
GACAGCAATGGAAATGCAAAAGGGATGGCAACGATCAATTATCTCGTTAATCGCATGCTA
AACTTCGGTTTGAAATCATCAGACAAGATCGATAAAGCAGTTTTCAAGAAGTTCTCAAAA
GTTGCATTAGACACATCACTTGGTCGTCTTTCACGTATTTTGGAAAAAGATCCTTACGTG
TTGGTTACTCAGAAACAAAAAGAATATGCAAATGGTGAAACTATTACAAGGGAAATTATT
ATCGGAATTATTACACAACGTGATTTGCTCAATTATGTTATGAAATTTCAACAAAAATAG
>g13122.t6 Gene=g13122 Length=421
MVLDAEEKGILKEGSTIIEPTSGNTGVGLAMACAVRGYRCIIVMPEKMSDEKVNTLKALG
AEIIRTPTEAAYDNPDSLIAVAQRLQKEIPNSWIPDQYRNCGNPLAHYDGTGAEILYQLD
GKVDMVVLGAGTGGTIAGVGRRIKEECPNCVIVGVDPEGSILAQPESLNESSVTMYEVEG
IGYDFIPTVLDRSVVDKWYKSNDKISLPMARRLIAEEGFLCGGSSGAAMSCAIAAAKDLT
EDQTCVVILPDNIRNYMTKFVVDNWLEARDLKNSVNTQDHPWWDNQVSNLHLRPPLTVTE
NVTCQEVIDIMKNEDIDQIPVIDSNGNAKGMATINYLVNRMLNFGLKSSDKIDKAVFKKF
SKVALDTSLGRLSRILEKDPYVLVTQKQKEYANGETITREIIIGIITQRDLLNYVMKFQQ
K
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13122.t6 | CDD | cd01561 | CBS_like | 1 | 258 | 0.0000000 |
| 8 | g13122.t6 | Gene3D | G3DSA:3.40.50.1100 | - | 1 | 104 | 0.0000000 |
| 9 | g13122.t6 | Gene3D | G3DSA:3.40.50.1100 | - | 105 | 259 | 0.0000000 |
| 7 | g13122.t6 | Gene3D | G3DSA:3.10.580.10 | - | 272 | 421 | 0.0000000 |
| 3 | g13122.t6 | PANTHER | PTHR10314:SF177 | CYSTATHIONINE BETA-SYNTHASE-RELATED | 1 | 348 | 0.0000000 |
| 4 | g13122.t6 | PANTHER | PTHR10314 | CYSTATHIONINE BETA-SYNTHASE | 1 | 348 | 0.0000000 |
| 2 | g13122.t6 | Pfam | PF00291 | Pyridoxal-phosphate dependent enzyme | 1 | 251 | 0.0000000 |
| 1 | g13122.t6 | Pfam | PF00571 | CBS domain | 290 | 337 | 0.0000011 |
| 14 | g13122.t6 | ProSiteProfiles | PS51371 | CBS domain profile. | 291 | 348 | 10.9690000 |
| 13 | g13122.t6 | ProSiteProfiles | PS51371 | CBS domain profile. | 352 | 421 | 5.7000000 |
| 12 | g13122.t6 | SMART | SM00116 | cbs_1 | 294 | 342 | 0.0000040 |
| 11 | g13122.t6 | SMART | SM00116 | cbs_1 | 359 | 416 | 34.0000000 |
| 5 | g13122.t6 | SUPERFAMILY | SSF53686 | Tryptophan synthase beta subunit-like PLP-dependent enzymes | 1 | 269 | 0.0000000 |
| 6 | g13122.t6 | SUPERFAMILY | SSF54631 | CBS-domain pair | 287 | 416 | 0.0000000 |
| 15 | g13122.t6 | TIGRFAM | TIGR01137 | cysta_beta: cystathionine beta-synthase | 1 | 416 | 0.0000000 |
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:0004122 | cystathionine beta-synthase activity | MF |
| GO:0005737 | cytoplasm | CC |
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.
