General information for g9850.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cysteine desulfurase, mitochondrial.
Parent gene
- The parent gene g9850 is located on chr_1: 5588364..5589828 (+ 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 | g9850 | g9850.t1 | TSS | g9850.t1 | 5586896 | 5586896 |
| chr_1 | g9850 | g9850.t1 | isoform | g9850.t1 | 5586951 | 5588364 |
| chr_1 | g9850 | g9850.t1 | exon | g9850.t1.exon1 | 5586951 | 5587035 |
| chr_1 | g9850 | g9850.t1 | cds | g9850.t1.CDS1 | 5586951 | 5587035 |
| chr_1 | g9850 | g9850.t1 | exon | g9850.t1.exon2 | 5587106 | 5588364 |
| chr_1 | g9850 | g9850.t1 | cds | g9850.t1.CDS2 | 5587106 | 5588364 |
| chr_1 | g9850 | g9850.t1 | TTS | g9850.t1 | 5588624 | 5588624 |
Sequences
>g9850.t1 Gene=g9850 Length=1344
ATGTTGCGTTTTTCTATAAGAAATAGCTCTTTAAATGAGCTCAAACAAACATCTAAAGCA
GTGTTTTGTCGATTTATATCTTCAGATAACGAAGGCAAAAACACTAAATTTAGTATCAAA
GACGAAACACTTGATGGCAGACCATTATATCTTGATGCTCAAGCAACAACACCACTTGAT
CCGAGAGTACTTGATAAGATGTTGCCATATTTAACAAATTATTACGGAAATCCACATTCA
AGAACTCACTATTATGGTTGGGAAACTGAAACTGCTGTTGAAAAAGCACGAAATCAAGTG
GCAAAATTAATCGGTGCTGATCCAAAAGAGATAATTTTCACATCAGGTGCAACCGAATCA
AATAATGTCGCAATTAAAGGAGTTGGAAGATTTTATGCTGAAAAAAAGAAACACATAATC
ACAACTCAAACGGAACATAAATGTGTACTCGATTCATGCAGAGCTTTGGAAGGTGAAGGA
TTCAAAGTAACTTATATGCCGGTCAATAGTAATGGTTTGATTGACATTGAAGCATTAGAA
AAAGCAATAACACCAGAAACGTCGCTTGTGTCAATCATGTCTGTGAATAATGAAATTGGA
GTAAGGCAACCAATTGAAGAAATTGGAAAATTGTGTAGATCAAAGAAAGTCTTTTTCCAT
ACAGATGCAGCTCAAGCTGTTGGAAAAATTCCTATAAATGTAAACGAAATGAACATCGAT
TTGATGTCAATTAGTGGTCATAAAATTTACGGACCAAAAGGAATTGGTTGCATTTATATT
CGTCGCAGACCTCGTGTAAGAATTGAGGCAATTCAGAGTGGTGGTGGACAAGAGAGAGGA
ATTCGAAGTGGAACACTTCCTGCGCCGCTTGTTGTTGGATTAGGAGCAGCATGTGAAATT
GCTGAAAAAGAAATGGACTATGATCATAAGAGAATTGAATTCTTATCAAAACGATTATTG
GATGGAATTTTAGGAAATTTGGAGCATGTTGTAAGAAATGGCGATCCTGAAAAATCATAT
CCAGGCTGTATCAATTTATCGTTTGCCTTTGTTGAGGGAGAATCATTGTTAATGGCATTA
AAAGATGTTGCTTTATCAAGTGGCAGTGCATGTACATCAGCATCACTTGAGCCATCATAT
GTTTTGAGAGCAATCGGAACAGAAGAAGACTTAGCACATAGCTCAATTCGTTTTGGAATT
GGAAGATTCACGACAATAGAAGAAGTTGATTATACAGTAGAGAAAACTATAAAACACGTA
AATAGATTAAGAGAAATGTCTCCATTATGGGAGATGGTACAGGAAGGCATTGACATTAAG
ACAATACAATGGTCACAGCATTAG
>g9850.t1 Gene=g9850 Length=447
MLRFSIRNSSLNELKQTSKAVFCRFISSDNEGKNTKFSIKDETLDGRPLYLDAQATTPLD
PRVLDKMLPYLTNYYGNPHSRTHYYGWETETAVEKARNQVAKLIGADPKEIIFTSGATES
NNVAIKGVGRFYAEKKKHIITTQTEHKCVLDSCRALEGEGFKVTYMPVNSNGLIDIEALE
KAITPETSLVSIMSVNNEIGVRQPIEEIGKLCRSKKVFFHTDAAQAVGKIPINVNEMNID
LMSISGHKIYGPKGIGCIYIRRRPRVRIEAIQSGGGQERGIRSGTLPAPLVVGLGAACEI
AEKEMDYDHKRIEFLSKRLLDGILGNLEHVVRNGDPEKSYPGCINLSFAFVEGESLLMAL
KDVALSSGSACTSASLEPSYVLRAIGTEEDLAHSSIRFGIGRFTTIEEVDYTVEKTIKHV
NRLREMSPLWEMVQEGIDIKTIQWSQH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9850.t1 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 50 | 418 | 2.0E-156 |
| 7 | g9850.t1 | Gene3D | G3DSA:3.40.640.10 | - | 60 | 304 | 2.0E-156 |
| 4 | g9850.t1 | Hamap | MF_00331 | Cysteine desulfurase IscS [iscS]. | 45 | 438 | 52.198936 |
| 2 | g9850.t1 | PANTHER | PTHR11601 | CYSTEINE DESULFURYLASE FAMILY MEMBER | 41 | 433 | 8.1E-204 |
| 3 | g9850.t1 | PANTHER | PTHR11601:SF34 | CYSTEINE DESULFURASE, MITOCHONDRIAL | 41 | 433 | 8.1E-204 |
| 8 | g9850.t1 | PIRSF | PIRSF005572 | NifS | 47 | 427 | 2.3E-127 |
| 1 | g9850.t1 | Pfam | PF00266 | Aminotransferase class-V | 50 | 411 | 1.7E-93 |
| 9 | g9850.t1 | ProSitePatterns | PS00595 | Aminotransferases class-V pyridoxal-phosphate attachment site. | 239 | 258 | - |
| 5 | g9850.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 48 | 434 | 1.45E-108 |
| 10 | g9850.t1 | TIGRFAM | TIGR02006 | IscS: cysteine desulfurase IscS | 48 | 447 | 7.4E-201 |
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:0044571 | [2Fe-2S] cluster assembly | BP |
| GO:0003824 | catalytic activity | MF |
| GO:0030170 | pyridoxal phosphate binding | MF |
| GO:0031071 | cysteine desulfurase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04487 (cysteine desulfurase)
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.
