General information for g3934.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cystathionine gamma-lyase.
Parent gene
- The parent gene g3934 is located on chr_3: 28991078..28992093 (+ 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_3 | g3934 | g3934.t9 | TSS | g3934.t9 | 28989283 | 28989283 |
| chr_3 | g3934 | g3934.t9 | isoform | g3934.t9 | 28989406 | 28992093 |
| chr_3 | g3934 | g3934.t9 | exon | g3934.t9.exon1 | 28989406 | 28989413 |
| chr_3 | g3934 | g3934.t9 | cds | g3934.t9.CDS1 | 28989406 | 28989413 |
| chr_3 | g3934 | g3934.t9 | exon | g3934.t9.exon2 | 28990546 | 28990647 |
| chr_3 | g3934 | g3934.t9 | cds | g3934.t9.CDS2 | 28990546 | 28990647 |
| chr_3 | g3934 | g3934.t9 | exon | g3934.t9.exon3 | 28990727 | 28991293 |
| chr_3 | g3934 | g3934.t9 | cds | g3934.t9.CDS3 | 28990727 | 28991293 |
| chr_3 | g3934 | g3934.t9 | exon | g3934.t9.exon4 | 28991350 | 28991408 |
| chr_3 | g3934 | g3934.t9 | cds | g3934.t9.CDS4 | 28991350 | 28991408 |
| chr_3 | g3934 | g3934.t9 | exon | g3934.t9.exon5 | 28991560 | 28991895 |
| chr_3 | g3934 | g3934.t9 | cds | g3934.t9.CDS5 | 28991560 | 28991895 |
| chr_3 | g3934 | g3934.t9 | exon | g3934.t9.exon6 | 28991981 | 28992093 |
| chr_3 | g3934 | g3934.t9 | cds | g3934.t9.CDS6 | 28991981 | 28992093 |
| chr_3 | g3934 | g3934.t9 | TTS | g3934.t9 | 28992182 | 28992182 |
Sequences
>g3934.t9 Gene=g3934 Length=1185
ATGTCCAACAGATTGACTTTTGGTGAAGAACTTGGATTTAAGAGGCAAAGTGAGGGGTTT
TCAACGAAAGCCATTCACTTGGGTCAAAAGCCCGAACAATGGAATAGCAGAGCTGTTGTG
CCTCCAATTTCATTGAGCACGACATTCAAACAAACAGCACCAGGCGTTCATTCGGGATTT
GAGTATAGTCGTTCAGGTAATCCAACTAGAAATGTCCTTGAAGCATGCCTCGCTGGTCTC
GACAATGCCAAATTCGCAGTAACATTTGCTAGTGGTCTTGGTACACAGACTGCCATCATC
AGCACACTTAAAACTGGCGATGGAATCATCACTGGTGATGATATATACGGCGGAACAAAT
CGATTGTTTCGTAATCTTGCCGCAAATATGGGAATTGAAGTTCAATTTGTTGATTTAACC
GATTTGAAAAACTTGGAGCAATCAATAAAACCAAATACAAAACTCGTATGGATGGAAACA
CCAACAAATCCGTGTATGAAAGTGATTGATATTAAAGGCGTTGCAGACATTGTTCATTCC
AAAACAAAAGCTTTCCTTGTTGTTGACAATACCTTCTTATCGGCTTACTTTCAACGTCCA
TTAGATTTGGGTGCTGATATTGTTATGTACAGTTTAACAAAATACATGAATGGTCATACT
GATGTAATTATGGGCAGCGCATCAACAAATAATGATGAATTGCATGAAAAACTCCGCTTT
TATCAAAATGCTACAGGCATCGTTCCATCGCCATTCGATTGCTACTTGGTGAATAGAAGT
TTGAAAACACTTTCATTGAGAATGGAGCGACACTTTTTCAACTCAGTTACAGTTGCAAAA
TGGCTTGAGGCACATCCAAAAGTTGAAAAAGTTTTGCATCCTGCATTGCTTTCTCATCCA
CAACATAAGCTTGCACTGACACAAACATTTGGCCATTCTGGAATAATGTCATTCTATATA
AAAGATGCATCTCTGGAGAAATCGTCAAAGTTTTTGCAAGTTTTAAAAGTTTTTACACTA
GCAGAAAGTCTCGGAGGCTATGAATCACTTGCAGGTATGCTAATTTGTCTCAAAGCACAA
CGAGCTGAATTAGGCATTACTGATGGACTTGTGCGTATTTCTGTCGGTCTTGAAGACTCA
CAGGATTTAATAAAAGACCTCGAGCAGGCTTTTGATTCCATTTAA
>g3934.t9 Gene=g3934 Length=394
MSNRLTFGEELGFKRQSEGFSTKAIHLGQKPEQWNSRAVVPPISLSTTFKQTAPGVHSGF
EYSRSGNPTRNVLEACLAGLDNAKFAVTFASGLGTQTAIISTLKTGDGIITGDDIYGGTN
RLFRNLAANMGIEVQFVDLTDLKNLEQSIKPNTKLVWMETPTNPCMKVIDIKGVADIVHS
KTKAFLVVDNTFLSAYFQRPLDLGADIVMYSLTKYMNGHTDVIMGSASTNNDELHEKLRF
YQNATGIVPSPFDCYLVNRSLKTLSLRMERHFFNSVTVAKWLEAHPKVEKVLHPALLSHP
QHKLALTQTFGHSGIMSFYIKDASLEKSSKFLQVLKVFTLAESLGGYESLAGMLICLKAQ
RAELGITDGLVRISVGLEDSQDLIKDLEQAFDSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3934.t9 | CDD | cd00614 | CGS_like | 38 | 392 | 2.88565E-172 |
| 7 | g3934.t9 | Coils | Coil | Coil | 377 | 394 | - |
| 6 | g3934.t9 | Gene3D | G3DSA:3.40.640.10 | - | 19 | 264 | 2.2E-90 |
| 5 | g3934.t9 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 265 | 394 | 9.9E-43 |
| 2 | g3934.t9 | PANTHER | PTHR11808:SF15 | CYSTATHIONINE GAMMA-LYASE | 15 | 393 | 9.8E-146 |
| 3 | g3934.t9 | PANTHER | PTHR11808 | TRANS-SULFURATION ENZYME FAMILY MEMBER | 15 | 393 | 9.8E-146 |
| 8 | g3934.t9 | PIRSF | PIRSF001434 | CGS | 9 | 394 | 4.4E-130 |
| 1 | g3934.t9 | Pfam | PF01053 | Cys/Met metabolism PLP-dependent enzyme | 21 | 391 | 1.0E-132 |
| 4 | g3934.t9 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 41 | 393 | 1.25E-103 |
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:0019346 | transsulfuration | BP |
| GO:0003824 | catalytic activity | MF |
| GO:0030170 | pyridoxal phosphate binding | MF |
KEGG
Orthology
- This transcript has been annotated with K01758 (cystathionine gamma-lyase)
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. There were no conditions that were differentially expressed