General information for g3934.t11
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.t11 | TSS | g3934.t11 | 28989283 | 28989283 |
| chr_3 | g3934 | g3934.t11 | isoform | g3934.t11 | 28989406 | 28992093 |
| chr_3 | g3934 | g3934.t11 | exon | g3934.t11.exon1 | 28989406 | 28989413 |
| chr_3 | g3934 | g3934.t11 | exon | g3934.t11.exon2 | 28990546 | 28990619 |
| chr_3 | g3934 | g3934.t11 | exon | g3934.t11.exon3 | 28990727 | 28991293 |
| chr_3 | g3934 | g3934.t11 | cds | g3934.t11.CDS1 | 28991004 | 28991293 |
| chr_3 | g3934 | g3934.t11 | exon | g3934.t11.exon4 | 28991350 | 28991408 |
| chr_3 | g3934 | g3934.t11 | cds | g3934.t11.CDS2 | 28991350 | 28991408 |
| chr_3 | g3934 | g3934.t11 | exon | g3934.t11.exon5 | 28991560 | 28991877 |
| chr_3 | g3934 | g3934.t11 | cds | g3934.t11.CDS3 | 28991560 | 28991877 |
| chr_3 | g3934 | g3934.t11 | exon | g3934.t11.exon6 | 28991945 | 28992093 |
| chr_3 | g3934 | g3934.t11 | cds | g3934.t11.CDS4 | 28991945 | 28992093 |
| chr_3 | g3934 | g3934.t11 | TTS | g3934.t11 | 28992182 | 28992182 |
Sequences
>g3934.t11 Gene=g3934 Length=1175
ATGTCCAACAGATTGACTTTTGGTGAAGAACTTGGATTTAAGAGGCAAAGTGAGGGGTTT
TCAACGAAAGCCATTCACTTGGAGCTGTTGTGCCTCCAATTTCATTGAGCACGACATTCA
AACAAACAGCACCAGGCGTTCATTCGGGATTTGAGTATAGTCGTTCAGGTAATCCAACTA
GAAATGTCCTTGAAGCATGCCTCGCTGGTCTCGACAATGCCAAATTCGCAGTAACATTTG
CTAGTGGTCTTGGTACACAGACTGCCATCATCAGCACACTTAAAACTGGCGATGGAATCA
TCACTGGTGATGATATATACGGCGGAACAAATCGATTGTTTCGTAATCTTGCCGCAAATA
TGGGAATTGAAGTTCAATTTGTTGATTTAACCGATTTGAAAAACTTGGAGCAATCAATAA
AACCAAATACAAAACTCGTATGGATGGAAACACCAACAAATCCGTGTATGAAAGTGATTG
ATATTAAAGGCGTTGCAGACATTGTTCATTCCAAAACAAAAGCTTTCCTTGTTGTTGACA
ATACCTTCTTATCGGCTTACTTTCAACGTCCATTAGATTTGGGTGCTGATATTGTTATGT
ACAGTTTAACAAAATACATGAATGGTCATACTGATGTAATTATGGGCAGCGCATCAACAA
ATAATGATGAATTGCATGAAAAACTCCGCTTTTATCAAAATGCTACAGGCATCGTTCCAT
CGCCATTCGATTGCTACTTGGTGAATAGAAGTTTGAAAACACTTTCATTGAGAATGGAGC
GACACTTTTTCAACTCAGTTACAGTTGCAAAATGGCTTGAGGCACATCCAAAAGTTGAAA
AAGTTTTGCATCCTGCATTGCTTTCTCATCCACAACATAAGCTTGCACTGACACAAACAT
TTGGCCATTCTGGAATAATGTCATTCTATATAAAAGATGCATCTCTGGAGAAATCGTCAA
AGTTTTTGCAAGTTTTAAAAGTTTTTACACTAGCAGAAAGTCTCGGAGGCTATGAATCAC
TTGCAGAATTGCCGAGCGTTATGACGCATGCATCCGTTCCAGAAGCACAACGAGCTGAAT
TAGGCATTACTGATGGACTTGTGCGTATTTCTGTCGGTCTTGAAGACTCACAGGATTTAA
TAAAAGACCTCGAGCAGGCTTTTGATTCCATTTAA
>g3934.t11 Gene=g3934 Length=271
MGIEVQFVDLTDLKNLEQSIKPNTKLVWMETPTNPCMKVIDIKGVADIVHSKTKAFLVVD
NTFLSAYFQRPLDLGADIVMYSLTKYMNGHTDVIMGSASTNNDELHEKLRFYQNATGIVP
SPFDCYLVNRSLKTLSLRMERHFFNSVTVAKWLEAHPKVEKVLHPALLSHPQHKLALTQT
FGHSGIMSFYIKDASLEKSSKFLQVLKVFTLAESLGGYESLAELPSVMTHASVPEAQRAE
LGITDGLVRISVGLEDSQDLIKDLEQAFDSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3934.t11 | CDD | cd00614 | CGS_like | 1 | 269 | 0 |
| 6 | g3934.t11 | Gene3D | G3DSA:3.40.640.10 | - | 1 | 135 | 0 |
| 5 | g3934.t11 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 136 | 271 | 0 |
| 2 | g3934.t11 | PANTHER | PTHR11808:SF15 | CYSTATHIONINE GAMMA-LYASE | 1 | 270 | 0 |
| 3 | g3934.t11 | PANTHER | PTHR11808 | TRANS-SULFURATION ENZYME FAMILY MEMBER | 1 | 270 | 0 |
| 1 | g3934.t11 | Pfam | PF01053 | Cys/Met metabolism PLP-dependent enzyme | 1 | 268 | 0 |
| 4 | g3934.t11 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 2 | 270 | 0 |
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 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. There were no conditions that were differentially expressed