General information for g11638.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sarcosine dehydrogenase, mitochondrial.
Parent gene
- The parent gene g11638 is located on chr_1: 17542437..17543168 (+ 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 | g11638 | g11638.t3 | TSS | g11638.t3 | 17538070 | 17538070 |
| chr_1 | g11638 | g11638.t3 | isoform | g11638.t3 | 17538144 | 17540947 |
| chr_1 | g11638 | g11638.t3 | exon | g11638.t3.exon1 | 17538144 | 17538258 |
| chr_1 | g11638 | g11638.t3 | exon | g11638.t3.exon2 | 17539196 | 17539307 |
| chr_1 | g11638 | g11638.t3 | cds | g11638.t3.CDS1 | 17539307 | 17539307 |
| chr_1 | g11638 | g11638.t3 | exon | g11638.t3.exon3 | 17539386 | 17539826 |
| chr_1 | g11638 | g11638.t3 | cds | g11638.t3.CDS2 | 17539386 | 17539826 |
| chr_1 | g11638 | g11638.t3 | exon | g11638.t3.exon4 | 17539906 | 17540100 |
| chr_1 | g11638 | g11638.t3 | cds | g11638.t3.CDS3 | 17539906 | 17540100 |
| chr_1 | g11638 | g11638.t3 | exon | g11638.t3.exon5 | 17540163 | 17540381 |
| chr_1 | g11638 | g11638.t3 | cds | g11638.t3.CDS4 | 17540163 | 17540381 |
| chr_1 | g11638 | g11638.t3 | exon | g11638.t3.exon6 | 17540610 | 17540675 |
| chr_1 | g11638 | g11638.t3 | cds | g11638.t3.CDS5 | 17540610 | 17540675 |
| chr_1 | g11638 | g11638.t3 | exon | g11638.t3.exon7 | 17540733 | 17540947 |
| chr_1 | g11638 | g11638.t3 | cds | g11638.t3.CDS6 | 17540733 | 17540947 |
| chr_1 | g11638 | g11638.t3 | TTS | g11638.t3 | NA | NA |
Sequences
>g11638.t3 Gene=g11638 Length=1363
ATGTTACGTTTTAAAAGGAAATTTATTGATTGCATCAAGATACAAAGGAAGCAATTTGTT
CGATGTTTTTCAACTCCAACTTCATTGCCTGAATATGCTGACGTTGTTATAATAGGTGGT
GGTGTTGCTGGATGCAGTACACTTTATCAATTAACTAAGCGTAATGTAAATGCAGTGTTA
TTAGAACGCGGTCAACTAACATGTGGTACTACATGGCATACCGGCAATGTGGCGTTTACG
ACCAAATGATGTTGAAATACAATTACTTGCCACAACTCGTGAATTATTGATGAGTTTAGA
ATCTGAAACTGGGTTGAACAGCGGTTGGATCAACAATGGCGGTTTATTCATCTCGCATTC
ACCGCAGCGCACAAATGAATATCGACGACTACAAACGCTTGGAAAAAGTTTTGGTATCGA
AAGTCGAATTCTGTCACCCCTTGAAGTTCAAAAAGAAGTTTTCCCATTGCTCGATCCGAA
ATCGTTTGAAAATGCTTTATTCTCACCGGGTGATGGAGTAGTTGATCCAGCAATGCTTTG
CACAGCTCTTACACGTGCTGCAACATCAAACGGTGGTAGAGTATTTGAAAATTGTGCGGT
TGACGAGTTGATTGTGGGTAAAACATTCCTCGGAGACAGGGAAATAAGAGGTGTTAAAAC
ACAAAATGGTATAATAAAGACAAATACAGTTGTAAATGCAACAGGAGTGTGGGGAAAAGA
TTTATTGGAGCCGTTAGATATACATTTACCTCTTGTGCCGATGCGTCATGCTTATGTCGT
TTCTGAGGCGATCAAAGAAGTGCAGGGAATGCCAAATGTTCGCGATCACGACTACAGTCT
CTATTTCCGTATTCAAGGTTATTGTCAATCTATACAAATGGGAGGTTATGAAAATAATCC
GATTTTACTTGACAAAGTTCCAGCTGATTTTCAATTTGGGCTTTATGATTTAGATTATTC
AGTTTTTGACACACACATTGAAGGCGCAGTGAAACTTTGTCCGACATTCGGTCAAGCAGG
TATAAAAAGTACTATTTGTGGCCCAGAAAGCTTCACGCCTGATCATAAGCCTCTAATGGT
AAATCCAATTCTTTCTGGATTATTTCATAGCTGTGGATACAATAGTGCTGGCATGATGTT
AAGTGCAGGTTGTGCAAAGCAATTAGCTTCATGGATTATACATGATAGACCAGATTTGCA
TTTATTTGCCTATGATATTAGAAGATTTACACCGAGACAAAGGAAAGCATATACTTGGGC
TATAGAAAGAAGTCATGAAGCCTACGCAAAAAATTATAGCATTGTCTTTCCAAATGACCA
GCCGCTTGCAGGAAGAAATTTTATTCAAGATCCATTCCATAAA
>g11638.t3 Gene=g11638 Length=379
MWRLRPNDVEIQLLATTRELLMSLESETGLNSGWINNGGLFISHSPQRTNEYRRLQTLGK
SFGIESRILSPLEVQKEVFPLLDPKSFENALFSPGDGVVDPAMLCTALTRAATSNGGRVF
ENCAVDELIVGKTFLGDREIRGVKTQNGIIKTNTVVNATGVWGKDLLEPLDIHLPLVPMR
HAYVVSEAIKEVQGMPNVRDHDYSLYFRIQGYCQSIQMGGYENNPILLDKVPADFQFGLY
DLDYSVFDTHIEGAVKLCPTFGQAGIKSTICGPESFTPDHKPLMVNPILSGLFHSCGYNS
AGMMLSAGCAKQLASWIIHDRPDLHLFAYDIRRFTPRQRKAYTWAIERSHEAYAKNYSIV
FPNDQPLAGRNFIQDPFHK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11638.t3 | Gene3D | G3DSA:3.50.50.60 | - | 1 | 335 | 0 |
| 8 | g11638.t3 | Gene3D | G3DSA:3.30.9.10 | - | 36 | 277 | 0 |
| 3 | g11638.t3 | PANTHER | PTHR13847 | SARCOSINE DEHYDROGENASE-RELATED | 1 | 379 | 0 |
| 4 | g11638.t3 | PANTHER | PTHR13847:SF200 | SARCOSINE DEHYDROGENASE, MITOCHONDRIAL | 1 | 379 | 0 |
| 2 | g11638.t3 | Pfam | PF01266 | FAD dependent oxidoreductase | 11 | 316 | 0 |
| 1 | g11638.t3 | Pfam | PF16350 | FAD dependent oxidoreductase central domain | 320 | 372 | 0 |
| 6 | g11638.t3 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 6 | 358 | 0 |
| 5 | g11638.t3 | SUPERFAMILY | SSF54373 | FAD-linked reductases, C-terminal domain | 176 | 277 | 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:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | 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