General information for g3933.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 g3933 is located on chr_3: 28987654..28988341 (+ 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 | g3933 | g3933.t1 | TSS | g3933.t1 | 28985355 | 28985355 |
| chr_3 | g3933 | g3933.t1 | isoform | g3933.t1 | 28985479 | 28988341 |
| chr_3 | g3933 | g3933.t1 | exon | g3933.t1.exon1 | 28985479 | 28985513 |
| chr_3 | g3933 | g3933.t1 | cds | g3933.t1.CDS1 | 28985479 | 28985513 |
| chr_3 | g3933 | g3933.t1 | exon | g3933.t1.exon2 | 28986607 | 28986705 |
| chr_3 | g3933 | g3933.t1 | cds | g3933.t1.CDS2 | 28986607 | 28986705 |
| chr_3 | g3933 | g3933.t1 | exon | g3933.t1.exon3 | 28987115 | 28987675 |
| chr_3 | g3933 | g3933.t1 | cds | g3933.t1.CDS3 | 28987115 | 28987675 |
| chr_3 | g3933 | g3933.t1 | exon | g3933.t1.exon4 | 28987737 | 28988098 |
| chr_3 | g3933 | g3933.t1 | cds | g3933.t1.CDS4 | 28987737 | 28988098 |
| chr_3 | g3933 | g3933.t1 | exon | g3933.t1.exon5 | 28988166 | 28988341 |
| chr_3 | g3933 | g3933.t1 | cds | g3933.t1.CDS5 | 28988166 | 28988341 |
| chr_3 | g3933 | g3933.t1 | TTS | g3933.t1 | 28988587 | 28988587 |
Sequences
>g3933.t1 Gene=g3933 Length=1233
ATGGGTTATCAAAGTGTCTCAAATGAACTAGCACCTTTGACAGAAAATGAGGCGATAGGA
TTTTTACGACAGGAATCTGGCTTTTCTACAAAAGCTATTCATGCAGGATATCGTCCTGAA
CAGTTATTGTGCCGATCTATAGTTGCACCTATTTATATGTCCGCATCATCATGCTCACAG
AGCAATGGAGTAAATGACGATTTGAATAAAAGCGAGAACCCAACAAAAATGATTCTTGAA
CAGACATTAGCAGCACTTGATAATGCAAAATATGCCCTTGTATTACCATCTGGCACAGCT
GCACAGAGCTGTATAATTGCGTCACTTAAAGCTGACGATGGAATTATTTGCGGACATAAT
ATTTATACAGGCACAATAGAGCTCTTTCGTGAAACAGCAGTAGATATTGGACTAAAGTGC
ATTTTTGTTGACATGACAAAACCCGAAGAACTGAGAAAAGCTCTGAGATCTCAAAAATCA
ACTAAAGTCGTTTGGGTTGAAACACCAAGCAACCCAATGATGCTTATAAGTGACATAAAA
ACAATTTCTGATATTGTGCATTGTGAAAGTAATGCTCTTGTTATCGTTGACAATACTCCA
TCAAGTTGCTATTTCCAGAGGCCTTTGGATTTTGGTGCAGATGTTGTCTCATATTCAATT
ACAAAATTCGTAAATGGACATAATGATGTTATTATGGGGAGCATTTCAACAAATAATCGA
GAATTTTATGAGAAAATAAGATTTACACAGGAAATTACTGGAATTACTTGTTCACCATTT
GATTGTGCTTTGGTGATACGAAGTTTGAAAACTTTGTCACTTCGCATGGAAAGACATTCT
TTAAATGCTTTATTGATAGCTCGCTACCTCGAACAACATCCTCGTGTTGAGAAAGTTCTT
CATCCTGGCCTAACATCACATCCACAACACAAAATTGCCATTTCACAAAGTTGTGGTCAT
GGTGGAAGTCTTTGTTTTTACATTAAAGATGGAACATTAGAACAAACAAAGAAATTCTTA
AAATTATTAAAAGTTTTTACTTGGGCTGACTCTTTAGGAGGATGCGAATCTTTAGCACAA
GCGCCACTTTTATGGTTTGTAGTACCGACATCTTTTTCTGATGAGGAAGTTCATGAGTTA
GGACTGGTGGAGAATTTAATACGTCTATCTTGCGGTCTCGAGGATGTGGCAATTTTAATT
GAGGATTTGAATCAGGCATTAAATGCTCTTTGA
>g3933.t1 Gene=g3933 Length=410
MGYQSVSNELAPLTENEAIGFLRQESGFSTKAIHAGYRPEQLLCRSIVAPIYMSASSCSQ
SNGVNDDLNKSENPTKMILEQTLAALDNAKYALVLPSGTAAQSCIIASLKADDGIICGHN
IYTGTIELFRETAVDIGLKCIFVDMTKPEELRKALRSQKSTKVVWVETPSNPMMLISDIK
TISDIVHCESNALVIVDNTPSSCYFQRPLDFGADVVSYSITKFVNGHNDVIMGSISTNNR
EFYEKIRFTQEITGITCSPFDCALVIRSLKTLSLRMERHSLNALLIARYLEQHPRVEKVL
HPGLTSHPQHKIAISQSCGHGGSLCFYIKDGTLEQTKKFLKLLKVFTWADSLGGCESLAQ
APLLWFVVPTSFSDEEVHELGLVENLIRLSCGLEDVAILIEDLNQALNAL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3933.t1 | CDD | cd00614 | CGS_like | 46 | 408 | 4.39039E-140 |
| 7 | g3933.t1 | Gene3D | G3DSA:3.40.640.10 | - | 27 | 271 | 2.9E-70 |
| 6 | g3933.t1 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 272 | 410 | 4.2E-42 |
| 2 | g3933.t1 | PANTHER | PTHR11808:SF15 | CYSTATHIONINE GAMMA-LYASE | 25 | 409 | 3.5E-116 |
| 3 | g3933.t1 | PANTHER | PTHR11808 | TRANS-SULFURATION ENZYME FAMILY MEMBER | 25 | 409 | 3.5E-116 |
| 8 | g3933.t1 | PIRSF | PIRSF001434 | CGS | 19 | 410 | 2.7E-114 |
| 1 | g3933.t1 | Pfam | PF01053 | Cys/Met metabolism PLP-dependent enzyme | 29 | 407 | 1.4E-111 |
| 5 | g3933.t1 | ProSitePatterns | PS00868 | Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. | 214 | 228 | - |
| 4 | g3933.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 73 | 408 | 1.48E-86 |
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