General information for g13123.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cystathionine beta-synthase.
Parent gene
- The parent gene g13123 is located on chr_1: 28048029..28049438 (+ 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 | g13123 | g13123.t5 | isoform | g13123.t5 | 28048027 | 28048905 |
| chr_1 | g13123 | g13123.t5 | exon | g13123.t5.exon1 | 28048027 | 28048905 |
| chr_1 | g13123 | g13123.t5 | cds | g13123.t5.CDS1 | 28048086 | 28048904 |
| chr_1 | g13123 | g13123.t5 | TTS | g13123.t5 | 28049656 | 28049656 |
| chr_1 | g13123 | g13123.t5 | TSS | g13123.t5 | NA | NA |
Sequences
>g13123.t5 Gene=g13123 Length=879
ACGCAAAGTGTGAATTCTTGAATCCAGGTGGTTCTGTCAAAGATCGAATTGGTTATCGCA
TGGTACTTGATGCTGAAGAAAAAGGTTTACTCAAGCCAGGATATACAATTATTGAGCCAA
CATCAGGAAATACAGGAATTGGCTTAGCTATGGCAAGTGCAGTTCGTGGTTATCGCTGCA
TTATCGTTTTGCCTGAGAAAAATTCAGATGAAAAAGTCAATGCACTCAAGGCATTTGGAG
CAGAAATAATTCGTACAAGAACTGAAGCTAAATTCGATGAGCCTGATTCATTAGTCGCTG
TTGCTCAACGCTTGCAGAAAGAAATTCCAAACTCTGTCATTTTAAATCAATACACAAATT
GCGGCAATCCATTGGCTCATTATGATGGAACTGGAAGTGAAATTTTGTATCAATTGGATG
GAAAAGTTGATATGGTCGTGCTTGGAGCAGGAACAGGCGGAACAATAACTGGTGTAGGTC
GTCGAATTAAAGAAGAATGTCCCAATTGCAAAATTATTGGAGTTGACCCAGAAGGTTCAA
TTTTAGCACAACCAGATTCTTTGAATAAAACGGATGTTGTGGTTTTTGATGTCGAAGGCA
TCGGTTACGATTTTATTCCGACTGTTCTAGATCGCGATATTGTTGATAAATGGATCAAAT
CTAATGATAAGATGGCTTTTCCAATGGCAAAACGTCTAATTCGCGAAGAAGGCTTTTTAT
GTGGTGGTTCATCTGGTGCAGCAATGGCAGCTGCAATCGAAGTCGCTAAAGATTTATCAG
AAGATCAAGTTTGTGTTGTCATTTGTCCGGACAATATTCGTAATTACATGAGTAAATTTT
TGGTTGACAATTGGATGGAAGCAAGAGGTTTGAAAGAAT
>g13123.t5 Gene=g13123 Length=273
MVLDAEEKGLLKPGYTIIEPTSGNTGIGLAMASAVRGYRCIIVLPEKNSDEKVNALKAFG
AEIIRTRTEAKFDEPDSLVAVAQRLQKEIPNSVILNQYTNCGNPLAHYDGTGSEILYQLD
GKVDMVVLGAGTGGTITGVGRRIKEECPNCKIIGVDPEGSILAQPDSLNKTDVVVFDVEG
IGYDFIPTVLDRDIVDKWIKSNDKMAFPMAKRLIREEGFLCGGSSGAAMAAAIEVAKDLS
EDQVCVVICPDNIRNYMSKFLVDNWMEARGLKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13123.t5 | CDD | cd01561 | CBS_like | 1 | 258 | 0 |
| 5 | g13123.t5 | Gene3D | G3DSA:3.40.50.1100 | - | 1 | 104 | 0 |
| 6 | g13123.t5 | Gene3D | G3DSA:3.40.50.1100 | - | 105 | 259 | 0 |
| 2 | g13123.t5 | PANTHER | PTHR10314:SF177 | CYSTATHIONINE BETA-SYNTHASE-RELATED | 1 | 269 | 0 |
| 3 | g13123.t5 | PANTHER | PTHR10314 | CYSTATHIONINE BETA-SYNTHASE | 1 | 269 | 0 |
| 1 | g13123.t5 | Pfam | PF00291 | Pyridoxal-phosphate dependent enzyme | 1 | 249 | 0 |
| 4 | g13123.t5 | SUPERFAMILY | SSF53686 | Tryptophan synthase beta subunit-like PLP-dependent enzymes | 1 | 270 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
