General information for g1838.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Twinkle protein, mitochondrial.
Parent gene
- The parent gene g1838 is located on chr_3: 13240012..13241299 (- 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 | g1838 | g1838.t1 | TTS | g1838.t1 | 13239076 | 13239076 |
| chr_3 | g1838 | g1838.t1 | isoform | g1838.t1 | 13239228 | 13241299 |
| chr_3 | g1838 | g1838.t1 | exon | g1838.t1.exon1 | 13239228 | 13239377 |
| chr_3 | g1838 | g1838.t1 | cds | g1838.t1.CDS1 | 13239228 | 13239377 |
| chr_3 | g1838 | g1838.t1 | exon | g1838.t1.exon2 | 13239440 | 13240977 |
| chr_3 | g1838 | g1838.t1 | cds | g1838.t1.CDS2 | 13239440 | 13240977 |
| chr_3 | g1838 | g1838.t1 | exon | g1838.t1.exon3 | 13241035 | 13241299 |
| chr_3 | g1838 | g1838.t1 | cds | g1838.t1.CDS3 | 13241035 | 13241299 |
| chr_3 | g1838 | g1838.t1 | TSS | g1838.t1 | 13241406 | 13241406 |
Sequences
>g1838.t1 Gene=g1838 Length=1953
ATGTTTGCTCATCGTGTTTTATTATCAAATCATTTAACGAAATCTTTCAATGTTTTGAAA
AAGGTATCATTCACAACAACAAATAATAATTTTAATAAAGATGATTCTAACGAGCATGCG
AGTGCCTCATTACTTCAAATTAAAAGGACACTAAAAATAGCAAATATCGAGTTTCAAGAT
AATGCTACAAATTTTAAAACTTCATGTCCAGTTTGTGAAAAATCATATTCTCAACAAAAG
GATATTTATATCAATAAAACAACTGGATATTTCATGTGTCCAAGTTGTAGATATGGTGGT
AAATTAGGATTAATTGAGAAATTCTTTACTACTTCACGATCCCAAAAAATAACCAATGAA
TTGAAAACTTATCAAAAGTTATTTCAAAACGCCAAAGAACAATATCAAAATGAAAATGAA
TTTGATTACCAATTTTATGAAAGAGAATATGAATTAGTGACTGAAGGAAATGCTGATAAT
ATATTTAAACAGTTTTCTATTGATGAAAGGATTTCAAAATCGTCATTAATTGGACTGAAT
AGTAGATATAATCAAGAAAGACAAGAACTTTTATTTCCTCTTATCGACATTATTGGTAAT
ATAGTTGGTTGTAAAATTGTCACAAAATTGAATGACACAGAATGGAAAGAAGTATCTTTA
CCCGATCAAAATGTCTCAGGTGTTATAATTTACAATAATTCAAAAATCAATAAATCAAAA
GACAAAGAACTACCTCAACAAAAGGCGATAGTTGTACTCAATATTCTTGACTTACTTGCA
TTAACAACAACTAAAATTAATGCAGCATTTATTTGTTTACCATATGGACTTAAGTTTCTT
CCTCAAGAGTGTCTTCCTATTCTTGATCAATATAATGAGCTCACACTTTGGTTTAATTAT
AACACTGCAGGCTGGGATGTAGCAAGAAATTTTGCCAAAAAACTTGATGAAAAACGTTGC
AAGTTTGTTAGACCAACTTCTGCTCATCCTACACCTTATAAAGCACTCATACAAAGTATT
GATATAAAAAGCATTTTTTCAAAGTCGACGTCAATTTTACATAAGGCAATTACAACATTT
GCTTCACTACGACAAGATGTTTTGAGTGACTTACAAAACATTGACAAAGTTCAAGGTGTA
AAATGGAAAAGATATCCTACACTCAATAAGTATTTAAAAGGTCATAGAAAAGGTGAACTT
ACAATTTTAACAGGTTCAACAGGTTGTGGAAAAACAACATTTATGTCTGAATATTCATTA
GATCTTGCAATTCAAGGTGTAAACACATTATGGGGATCTTTTGAAATAAGAAATACACGA
TTAGCTACAACTTTATTAAGACAATATTGTGGAAAACCATTATTAGATTCAGTGTCAGAT
GAAAATCTTATAGAATTTGAACAATGGGCAAACAAATTTGAAGAGCTTCCTATATATTTT
ATGACATTTCATGGAAGTCAGCCCATAAAAGTAGTAATGGAAGCAATTGAACATGCACAA
TACGTTCACGATATTAATCATGTCATTATTGATAATGTTCAATTTATGATGGGTACGAGC
GAAGAATCAAAGCATTTAGATAGGTTTTGGAAACAAGATGTCATAATTGCAGCTTTCAGA
ACTTTTGCAACGAAAAAAAATTGTCATGTAACTTTAGTAATTCATCCTAGAAAAGAAAAA
GATAATGAAGATTTGACTACCCAGTCAATATTTGGCGGAGCTAAAGCTACACAAGAAGCT
GATAATGTTCTTATTATTCAAGACAAACGATTAACTTCAGTCCGTGGCAAGAAATATCTA
CAGATTGCAAAAAATCGATATTCTGGAGATCTCGGAATAATGCCGCTCGAATTTGATAAA
GAAAGTTTAAGTTATGCTCATAAAACAAAGAAAAAGGTGGAAAACACTGATTCATCACAA
AGTATATCATCACCACCATTTGAAAAAATTTAA
>g1838.t1 Gene=g1838 Length=650
MFAHRVLLSNHLTKSFNVLKKVSFTTTNNNFNKDDSNEHASASLLQIKRTLKIANIEFQD
NATNFKTSCPVCEKSYSQQKDIYINKTTGYFMCPSCRYGGKLGLIEKFFTTSRSQKITNE
LKTYQKLFQNAKEQYQNENEFDYQFYEREYELVTEGNADNIFKQFSIDERISKSSLIGLN
SRYNQERQELLFPLIDIIGNIVGCKIVTKLNDTEWKEVSLPDQNVSGVIIYNNSKINKSK
DKELPQQKAIVVLNILDLLALTTTKINAAFICLPYGLKFLPQECLPILDQYNELTLWFNY
NTAGWDVARNFAKKLDEKRCKFVRPTSAHPTPYKALIQSIDIKSIFSKSTSILHKAITTF
ASLRQDVLSDLQNIDKVQGVKWKRYPTLNKYLKGHRKGELTILTGSTGCGKTTFMSEYSL
DLAIQGVNTLWGSFEIRNTRLATTLLRQYCGKPLLDSVSDENLIEFEQWANKFEELPIYF
MTFHGSQPIKVVMEAIEHAQYVHDINHVIIDNVQFMMGTSEESKHLDRFWKQDVIIAAFR
TFATKKNCHVTLVIHPRKEKDNEDLTTQSIFGGAKATQEADNVLIIQDKRLTSVRGKKYL
QIAKNRYSGDLGIMPLEFDKESLSYAHKTKKKVENTDSSQSISSPPFEKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1838.t1 | CDD | cd01122 | GP4d_helicase | 366 | 625 | 1.18559E-94 |
| 7 | g1838.t1 | Coils | Coil | Coil | 114 | 134 | - |
| 6 | g1838.t1 | Gene3D | G3DSA:3.40.50.300 | - | 364 | 628 | 3.8E-48 |
| 9 | g1838.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 629 | 650 | - |
| 10 | g1838.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 636 | 650 | - |
| 2 | g1838.t1 | PANTHER | PTHR12873:SF0 | TWINKLE PROTEIN, MITOCHONDRIAL | 26 | 627 | 1.4E-139 |
| 3 | g1838.t1 | PANTHER | PTHR12873 | T7-LIKE MITOCHONDRIAL DNA HELICASE | 26 | 627 | 1.4E-139 |
| 1 | g1838.t1 | Pfam | PF13481 | AAA domain | 377 | 560 | 9.7E-26 |
| 11 | g1838.t1 | ProSiteProfiles | PS51199 | Superfamily 4 helicase domain profile. | 374 | 632 | 49.498 |
| 4 | g1838.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 360 | 611 | 7.8E-24 |
| 5 | g1838.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 24 | - |
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:0005524 | ATP binding | MF |
| GO:0006260 | DNA replication | BP |
| GO:0003678 | DNA helicase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K17680 (twinkle protein)
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.
