General information for g3934.t1
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.t1 | TSS | g3934.t1 | 28989283 | 28989283 |
| chr_3 | g3934 | g3934.t1 | isoform | g3934.t1 | 28989406 | 28992093 |
| chr_3 | g3934 | g3934.t1 | exon | g3934.t1.exon1 | 28989406 | 28989413 |
| chr_3 | g3934 | g3934.t1 | cds | g3934.t1.CDS1 | 28989406 | 28989413 |
| chr_3 | g3934 | g3934.t1 | exon | g3934.t1.exon2 | 28990549 | 28990647 |
| chr_3 | g3934 | g3934.t1 | cds | g3934.t1.CDS2 | 28990549 | 28990647 |
| chr_3 | g3934 | g3934.t1 | exon | g3934.t1.exon3 | 28990727 | 28991293 |
| chr_3 | g3934 | g3934.t1 | cds | g3934.t1.CDS3 | 28990727 | 28991293 |
| chr_3 | g3934 | g3934.t1 | exon | g3934.t1.exon4 | 28991350 | 28991408 |
| chr_3 | g3934 | g3934.t1 | cds | g3934.t1.CDS4 | 28991350 | 28991408 |
| chr_3 | g3934 | g3934.t1 | exon | g3934.t1.exon5 | 28991560 | 28991877 |
| chr_3 | g3934 | g3934.t1 | cds | g3934.t1.CDS5 | 28991560 | 28991877 |
| chr_3 | g3934 | g3934.t1 | exon | g3934.t1.exon6 | 28991945 | 28992093 |
| chr_3 | g3934 | g3934.t1 | cds | g3934.t1.CDS6 | 28991945 | 28992093 |
| chr_3 | g3934 | g3934.t1 | TTS | g3934.t1 | 28992182 | 28992182 |
Sequences
>g3934.t1 Gene=g3934 Length=1200
ATGTCCAAATTGACTTTTGGTGAAGAACTTGGATTTAAGAGGCAAAGTGAGGGGTTTTCA
ACGAAAGCCATTCACTTGGGTCAAAAGCCCGAACAATGGAATAGCAGAGCTGTTGTGCCT
CCAATTTCATTGAGCACGACATTCAAACAAACAGCACCAGGCGTTCATTCGGGATTTGAG
TATAGTCGTTCAGGTAATCCAACTAGAAATGTCCTTGAAGCATGCCTCGCTGGTCTCGAC
AATGCCAAATTCGCAGTAACATTTGCTAGTGGTCTTGGTACACAGACTGCCATCATCAGC
ACACTTAAAACTGGCGATGGAATCATCACTGGTGATGATATATACGGCGGAACAAATCGA
TTGTTTCGTAATCTTGCCGCAAATATGGGAATTGAAGTTCAATTTGTTGATTTAACCGAT
TTGAAAAACTTGGAGCAATCAATAAAACCAAATACAAAACTCGTATGGATGGAAACACCA
ACAAATCCGTGTATGAAAGTGATTGATATTAAAGGCGTTGCAGACATTGTTCATTCCAAA
ACAAAAGCTTTCCTTGTTGTTGACAATACCTTCTTATCGGCTTACTTTCAACGTCCATTA
GATTTGGGTGCTGATATTGTTATGTACAGTTTAACAAAATACATGAATGGTCATACTGAT
GTAATTATGGGCAGCGCATCAACAAATAATGATGAATTGCATGAAAAACTCCGCTTTTAT
CAAAATGCTACAGGCATCGTTCCATCGCCATTCGATTGCTACTTGGTGAATAGAAGTTTG
AAAACACTTTCATTGAGAATGGAGCGACACTTTTTCAACTCAGTTACAGTTGCAAAATGG
CTTGAGGCACATCCAAAAGTTGAAAAAGTTTTGCATCCTGCATTGCTTTCTCATCCACAA
CATAAGCTTGCACTGACACAAACATTTGGCCATTCTGGAATAATGTCATTCTATATAAAA
GATGCATCTCTGGAGAAATCGTCAAAGTTTTTGCAAGTTTTAAAAGTTTTTACACTAGCA
GAAAGTCTCGGAGGCTATGAATCACTTGCAGAATTGCCGAGCGTTATGACGCATGCATCC
GTTCCAGAAGCACAACGAGCTGAATTAGGCATTACTGATGGACTTGTGCGTATTTCTGTC
GGTCTTGAAGACTCACAGGATTTAATAAAAGACCTCGAGCAGGCTTTTGATTCCATTTAA
>g3934.t1 Gene=g3934 Length=399
MSKLTFGEELGFKRQSEGFSTKAIHLGQKPEQWNSRAVVPPISLSTTFKQTAPGVHSGFE
YSRSGNPTRNVLEACLAGLDNAKFAVTFASGLGTQTAIISTLKTGDGIITGDDIYGGTNR
LFRNLAANMGIEVQFVDLTDLKNLEQSIKPNTKLVWMETPTNPCMKVIDIKGVADIVHSK
TKAFLVVDNTFLSAYFQRPLDLGADIVMYSLTKYMNGHTDVIMGSASTNNDELHEKLRFY
QNATGIVPSPFDCYLVNRSLKTLSLRMERHFFNSVTVAKWLEAHPKVEKVLHPALLSHPQ
HKLALTQTFGHSGIMSFYIKDASLEKSSKFLQVLKVFTLAESLGGYESLAELPSVMTHAS
VPEAQRAELGITDGLVRISVGLEDSQDLIKDLEQAFDSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3934.t1 | CDD | cd00614 | CGS_like | 37 | 397 | 0 |
| 6 | g3934.t1 | Gene3D | G3DSA:3.40.640.10 | - | 18 | 263 | 0 |
| 5 | g3934.t1 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 264 | 399 | 0 |
| 2 | g3934.t1 | PANTHER | PTHR11808:SF15 | CYSTATHIONINE GAMMA-LYASE | 14 | 398 | 0 |
| 3 | g3934.t1 | PANTHER | PTHR11808 | TRANS-SULFURATION ENZYME FAMILY MEMBER | 14 | 398 | 0 |
| 7 | g3934.t1 | PIRSF | PIRSF001434 | CGS | 8 | 399 | 0 |
| 1 | g3934.t1 | Pfam | PF01053 | Cys/Met metabolism PLP-dependent enzyme | 20 | 396 | 0 |
| 4 | g3934.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 40 | 398 | 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 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