General information for g13122.t2
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.t2 | isoform | g13122.t2 | 28042939 | 28044442 |
| chr_1 | g13122 | g13122.t2 | exon | g13122.t2.exon1 | 28042939 | 28043040 |
| chr_1 | g13122 | g13122.t2 | TSS | g13122.t2 | 28042969 | 28042969 |
| chr_1 | g13122 | g13122.t2 | exon | g13122.t2.exon2 | 28043146 | 28043403 |
| chr_1 | g13122 | g13122.t2 | cds | g13122.t2.CDS1 | 28043207 | 28043403 |
| chr_1 | g13122 | g13122.t2 | exon | g13122.t2.exon3 | 28043598 | 28043704 |
| chr_1 | g13122 | g13122.t2 | cds | g13122.t2.CDS2 | 28043598 | 28043704 |
| chr_1 | g13122 | g13122.t2 | exon | g13122.t2.exon4 | 28043772 | 28044442 |
| chr_1 | g13122 | g13122.t2 | cds | g13122.t2.CDS3 | 28043772 | 28044442 |
| chr_1 | g13122 | g13122.t2 | TTS | g13122.t2 | 28045345 | 28045345 |
Sequences
>g13122.t2 Gene=g13122 Length=1138
AAAAGAATACGTAGAACGCCGGCATATGCTCATTCTATACGAAGTTGTTGAAGTGATCGG
TCTGCTGACGTTTCAGTTTCTTATTCTGTGAAGCATTTTAATTCAAAAGATCATTTACGT
CATTTATTTCTTGAGTTGAAAACAAAAAGAAGATAAAAAGAACATGTCTGAAACTAAGGA
AAAAATTGTTAATGGCACTTCTGCTGCGACAAAAAATGGTCAGCTTTGTCCATATAAAAT
ATTGAAAGATCTTCCTAAAGTTCTTCCATCGGATTTTATTTTGCCAAATTTGCCATCAAG
ATGTACATGGACAAGTGATAAGAACAAGCAAGCTGCATCACCTCATCCAAAAAGGACCTT
CAAAGAAAGACCAAAAGTTTGTGAAAATGTCTTGGAAGCAATTGGAATGACACCATTAGT
CAAATTGAATCACATTCCACAATCATTGGGTATCAAATGTCAAATGTATGCAAAGTGTGA
ATTCTTGAATCCAGGTGGTTCTGTCAAAGATAGAATTGGTTATCGCATGGTACTTGATGC
TGAAGAGAAAGGAATTTTGAAAGAAGGTTCAACAATTATTGAGCCAACATCAGGAAATAC
TGGTGTGGGCTTAGCTATGGCATGTGCTGTTCGTGGTTATCGCTGTATCATTGTTATGCC
CGAGAAAATGTCTGACGAAAAGGTCAACACTTTGAAAGCTCTCGGGGCAGAGATCATTCG
TACGCCAACTGAAGCCGCCTATGATAATCCCGATTCACTCATTGCTGTTGCACAGCGTTT
GCAAAAAGAAATTCCAAATTCATGGATTCCTGATCAATATCGCAATTGTGGTAATCCATT
GGCTCATTATGATGGAACTGGTGCTGAAATTTTGTATCAATTGGATGGCAAAGTTGATAT
GGTTGTGCTTGGAGCAGGAACAGGCGGAACAATTGCTGGTGTAGGTCGTCGAATTAAAGA
AGAATGTCCCAATTGTGTTATTGTTGGTGTTGACCCAGAAGGTTCAATTTTAGCACAACC
TGAATCACTCAATGAATCAAGTGTCACAATGTATGAAGTTGAAGGAATTGGTTACGATTT
TATTCCGACAGTACTTGATCGTTCAGTTGTTGATAAATGGTACAAATCAAACGACAAA
>g13122.t2 Gene=g13122 Length=325
MSETKEKIVNGTSAATKNGQLCPYKILKDLPKVLPSDFILPNLPSRCTWTSDKNKQAASP
HPKRTFKERPKVCENVLEAIGMTPLVKLNHIPQSLGIKCQMYAKCEFLNPGGSVKDRIGY
RMVLDAEEKGILKEGSTIIEPTSGNTGVGLAMACAVRGYRCIIVMPEKMSDEKVNTLKAL
GAEIIRTPTEAAYDNPDSLIAVAQRLQKEIPNSWIPDQYRNCGNPLAHYDGTGAEILYQL
DGKVDMVVLGAGTGGTIAGVGRRIKEECPNCVIVGVDPEGSILAQPESLNESSVTMYEVE
GIGYDFIPTVLDRSVVDKWYKSNDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13122.t2 | CDD | cd01561 | CBS_like | 81 | 325 | 1.79208E-115 |
| 7 | g13122.t2 | Gene3D | G3DSA:3.40.50.1100 | - | 80 | 324 | 1.5E-107 |
| 6 | g13122.t2 | Gene3D | G3DSA:3.40.50.1100 | - | 112 | 225 | 1.5E-107 |
| 2 | g13122.t2 | PANTHER | PTHR10314:SF177 | CYSTATHIONINE BETA-SYNTHASE-RELATED | 34 | 325 | 7.9E-149 |
| 3 | g13122.t2 | PANTHER | PTHR10314 | CYSTATHIONINE BETA-SYNTHASE | 34 | 325 | 7.9E-149 |
| 1 | g13122.t2 | Pfam | PF00291 | Pyridoxal-phosphate dependent enzyme | 78 | 282 | 1.9E-55 |
| 5 | g13122.t2 | ProSitePatterns | PS00901 | Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. | 104 | 122 | - |
| 4 | g13122.t2 | SUPERFAMILY | SSF53686 | Tryptophan synthase beta subunit-like PLP-dependent enzymes | 63 | 324 | 5.76E-81 |
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:0006535 | cysteine biosynthetic process from serine | BP |
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.
