General information for g11638.t1
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.t1 | TSS | g11638.t1 | 17538070 | 17538070 |
| chr_1 | g11638 | g11638.t1 | isoform | g11638.t1 | 17538144 | 17542861 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon1 | 17538144 | 17538258 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS1 | 17538144 | 17538258 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon2 | 17539196 | 17539303 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS2 | 17539196 | 17539303 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon3 | 17539377 | 17539826 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS3 | 17539377 | 17539826 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon4 | 17539906 | 17540094 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS4 | 17539906 | 17540094 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon5 | 17540163 | 17540377 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS5 | 17540163 | 17540377 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon6 | 17540603 | 17540675 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS6 | 17540603 | 17540675 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon7 | 17540733 | 17540947 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS7 | 17540733 | 17540947 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon8 | 17541014 | 17541053 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS8 | 17541014 | 17541053 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon9 | 17541170 | 17541327 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS9 | 17541170 | 17541327 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon10 | 17541393 | 17541535 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS10 | 17541393 | 17541535 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon11 | 17541596 | 17541708 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS11 | 17541596 | 17541708 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon12 | 17541784 | 17541915 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS12 | 17541784 | 17541915 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon13 | 17541983 | 17542264 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS13 | 17541983 | 17542264 |
| chr_1 | g11638 | g11638.t1 | exon | g11638.t1.exon14 | 17542428 | 17542861 |
| chr_1 | g11638 | g11638.t1 | cds | g11638.t1.CDS14 | 17542428 | 17542861 |
| chr_1 | g11638 | g11638.t1 | TTS | g11638.t1 | 17543167 | 17543167 |
Sequences
>g11638.t1 Gene=g11638 Length=2667
ATGTTACGTTTTAAAAGGAAATTTATTGATTGCATCAAGATACAAAGGAAGCAATTTGTT
CGATGTTTTTCAACTCCAACTTCATTGCCTGAATATGCTGACGTTGTTATAATAGGTGGT
GGTGTTGCTGGATGCAGTACACTTTATCAATTAACTAAGCGTAATGTAAATGCAGTGTTA
TTAGAACGCGGTCAACTAACATGTGGTACTACATGGCATACCGCCGGCTTAGTGTGGCGT
TTACGACCAAATGATGTTGAAATACAATTACTTGCCACAACTCGTGAATTATTGATGAGT
TTAGAATCTGAAACTGGGTTGAACAGCGGTTGGATCAACAATGGCGGTTTATTCATCTCG
CATTCACCGCAGCGCACAAATGAATATCGACGACTACAAACGCTTGGAAAAAGTTTTGGT
ATCGAAAGTCGAATTCTGTCACCCCTTGAAGTTCAAAAAGAAGTTTTCCCATTGCTCGAT
CCGAAATCGTTTGAAAATGCTTTATTCTCACCGGGTGATGGAGTAGTTGATCCAGCAATG
CTTTGCACAGCTCTTACACGTGCTGCAACATCAAACGGTGGTAGAGTATTTGAAAATTGT
GCGGTTGACGAGTTGATTGTGGGTAAAACATTCCTCGGAGACAGGGAAATAAGAGGTGTT
AAAACACAAAATGGTATAATAAAGACAAATACAGTTGTAAATGCAACAGGAGTGTGGGGA
AAAGATTTATTGGAGCCGTTAGATATACATTTACCTCTTGTGCCGATGCGTCATGCTTAT
GTCGTTTCTGAGGCGATCAAAGAAGTGCAGGGAATGCCAAATGTTCGCGATCACGACTAC
AGTCTCTATTTCCGTATTCAAGGTCAATCTATACAAATGGGAGGTTATGAAAATAATCCG
ATTTTACTTGACAAAGTTCCAGCTGATTTTCAATTTGGGCTTTATGATTTAGATTATTCA
GTTTTTGACACACACATTGAAGGCGCAGTGAAACTTTGTCCGACATTCGGTCAAGCAGGT
ATAAAAAGTACTATTTGTGGCCCAGAAAGCTTCACGCCTGATCATAAGCCTCTAATGGGC
CCAGATCCAATTCTTTCTGGATTATTTCATAGCTGTGGATACAATAGTGCTGGCATGATG
TTAAGTGCAGGTTGTGCAAAGCAATTAGCTTCATGGATTATACATGATAGACCAGATTTG
CATTTATTTGCCTATGATATTAGAAGATTTACACCGAGACAAAGGAAAGCATATACTTGG
GCTATAGAAAGAAGTCATGAAGCCTACGCAAAAAATTATAGCATTGTCTTTCCAAATGAC
CAGCCGCTTGCAGGAAGAAATTTTATTCAAGATCCATTCCATAAAATTCTCGTAAATTAT
GGTGCAGTAATGGAAGAAAAGAGCGGATTTGAGCGACCTGGCTATTACATTCATGATGGT
ATAGCTCCCGTTCAGAAATACGATTATTATGGCTATTATGGTCGCGAGAAAAATAAGAAT
ACTTGCTATGCTGAGAAACTTGCTGGTGATTATAAATTTGAGTTTTCAGACCATCATGAT
CTTATTAGTGAAGAAGCTCATTCGTGTCGAGAAAATGCAGTGGTATTTAATTTGAGTTAT
TTTTGTAAAGTATTCATTACTGGTTCACAAGCTGAAGAAGCAGCAAAATGGATTTTCACA
GCAGATCTAAATAAGCCATTTAATAAAACGATCTATACGTGTGCATTAAATAACCGTGGT
GGTGTCGAAATTGATTTGACAGTTACAGGAATAGAATCTGGTGTTGGTGAACTTCATGAT
CCTATATTTAAGGGCCGTGGATATTATGCTGTTTGTGGTGGAGCTTCTTCCTATCATTCC
ATAGCACACATGCAAGAGGCGATTCGTGAGAAAGGTTTCCGCGCTAAACTCTGTGATGTA
ACACATGAACTTGGCATTCTATCATTACAAGGTCCAAAGAGCAGAGACATACTTTCATTG
ATTACTGATTACGACTTATCGAATGAAAATATGCCGCCAAACTCGGCTGCTATAATGAAG
ATTAAAGGACTCAAGGGAGAAGTATTTAACGTTCGAGTGCTTAGAGTCAGTTTTGTCGGT
GAATTGGGATTTGAGCTTCACATTCCAAAAGAGTCATGTGCTCATGTTTACAATATTTTA
ATGCATGCTGGTGGATCATTTAACTTGAAAAATGCTGGCTATCGGTCACTTTATTCCCTC
AGTAGTGAAAAAGGTTATCATTTATGGGGCTTTGATTTGAGATCAGATGACACGCCTATA
GAAGCTAATCTAGGCTTCGTATGTCGAAAGGATGCTGTTAGTTATAAAGGAAAAGAAGTT
ATTCTAGAACAACAAAGAAATGGGACTCAAAAGCGTCTCGTTTATCTGACATTAAAAGAG
AAAATACCATTATGGGGTCTGGAGGCTGTTTATCGAAATAATAAAATTGTCGGACACTTG
AGACGCGGTGAATTCGCATACATACTCGATTGTTCACTCGGACAATGTTATATTAAGCGT
ACAGACTCTAAAGCAATTGATATCGATTACATAATGTCAGGAAAATATCAGATTGAAGTG
ATGGGAAAATTATACGATGCTGATATTCATCTGAGATCTCCATTTGATCCAAAAGGTCGA
AGAATTCTCGGCGAATATAAAAGTTAG
>g11638.t1 Gene=g11638 Length=888
MLRFKRKFIDCIKIQRKQFVRCFSTPTSLPEYADVVIIGGGVAGCSTLYQLTKRNVNAVL
LERGQLTCGTTWHTAGLVWRLRPNDVEIQLLATTRELLMSLESETGLNSGWINNGGLFIS
HSPQRTNEYRRLQTLGKSFGIESRILSPLEVQKEVFPLLDPKSFENALFSPGDGVVDPAM
LCTALTRAATSNGGRVFENCAVDELIVGKTFLGDREIRGVKTQNGIIKTNTVVNATGVWG
KDLLEPLDIHLPLVPMRHAYVVSEAIKEVQGMPNVRDHDYSLYFRIQGQSIQMGGYENNP
ILLDKVPADFQFGLYDLDYSVFDTHIEGAVKLCPTFGQAGIKSTICGPESFTPDHKPLMG
PDPILSGLFHSCGYNSAGMMLSAGCAKQLASWIIHDRPDLHLFAYDIRRFTPRQRKAYTW
AIERSHEAYAKNYSIVFPNDQPLAGRNFIQDPFHKILVNYGAVMEEKSGFERPGYYIHDG
IAPVQKYDYYGYYGREKNKNTCYAEKLAGDYKFEFSDHHDLISEEAHSCRENAVVFNLSY
FCKVFITGSQAEEAAKWIFTADLNKPFNKTIYTCALNNRGGVEIDLTVTGIESGVGELHD
PIFKGRGYYAVCGGASSYHSIAHMQEAIREKGFRAKLCDVTHELGILSLQGPKSRDILSL
ITDYDLSNENMPPNSAAIMKIKGLKGEVFNVRVLRVSFVGELGFELHIPKESCAHVYNIL
MHAGGSFNLKNAGYRSLYSLSSEKGYHLWGFDLRSDDTPIEANLGFVCRKDAVSYKGKEV
ILEQQRNGTQKRLVYLTLKEKIPLWGLEAVYRNNKIVGHLRRGEFAYILDCSLGQCYIKR
TDSKAIDIDYIMSGKYQIEVMGKLYDADIHLRSPFDPKGRRILGEYKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11638.t1 | Gene3D | G3DSA:3.50.50.60 | - | 35 | 411 | 0 |
| 14 | g11638.t1 | Gene3D | G3DSA:3.30.9.10 | - | 113 | 352 | 0 |
| 11 | g11638.t1 | Gene3D | G3DSA:3.30.1360.120 | Probable tRNA modification gtpase trme; domain 1 | 446 | 756 | 0 |
| 13 | g11638.t1 | Gene3D | G3DSA:3.30.70.1400 | - | 541 | 780 | 0 |
| 15 | g11638.t1 | Gene3D | G3DSA:2.40.30.110 | - | 787 | 869 | 0 |
| 5 | g11638.t1 | PANTHER | PTHR13847 | SARCOSINE DEHYDROGENASE-RELATED | 20 | 565 | 0 |
| 6 | g11638.t1 | PANTHER | PTHR13847:SF200 | SARCOSINE DEHYDROGENASE, MITOCHONDRIAL | 20 | 565 | 0 |
| 3 | g11638.t1 | Pfam | PF01266 | FAD dependent oxidoreductase | 34 | 392 | 0 |
| 2 | g11638.t1 | Pfam | PF16350 | FAD dependent oxidoreductase central domain | 396 | 448 | 0 |
| 4 | g11638.t1 | Pfam | PF01571 | Aminomethyltransferase folate-binding domain | 454 | 767 | 0 |
| 1 | g11638.t1 | Pfam | PF08669 | Glycine cleavage T-protein C-terminal barrel domain | 791 | 876 | 0 |
| 10 | g11638.t1 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 34 | 432 | 0 |
| 9 | g11638.t1 | SUPERFAMILY | SSF54373 | FAD-linked reductases, C-terminal domain | 253 | 352 | 0 |
| 8 | g11638.t1 | SUPERFAMILY | SSF103025 | Folate-binding domain | 446 | 788 | 0 |
| 7 | g11638.t1 | SUPERFAMILY | SSF101790 | Aminomethyltransferase beta-barrel domain | 791 | 882 | 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:0005515 | protein binding | MF |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00314 (sarcosine dehydrogenase)
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.
