General information for g1838.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t2 | TTS | g1838.t2 | 13239076 | 13239076 |
| chr_3 | g1838 | g1838.t2 | isoform | g1838.t2 | 13240012 | 13241299 |
| chr_3 | g1838 | g1838.t2 | exon | g1838.t2.exon1 | 13240012 | 13240977 |
| chr_3 | g1838 | g1838.t2 | cds | g1838.t2.CDS1 | 13240013 | 13240977 |
| chr_3 | g1838 | g1838.t2 | exon | g1838.t2.exon2 | 13241035 | 13241299 |
| chr_3 | g1838 | g1838.t2 | cds | g1838.t2.CDS2 | 13241035 | 13241299 |
| chr_3 | g1838 | g1838.t2 | TSS | g1838.t2 | 13241406 | 13241406 |
Sequences
>g1838.t2 Gene=g1838 Length=1231
ATGTTTGCTCATCGTGTTTTATTATCAAATCATTTAACGAAATCTTTCAATGTTTTGAAA
AAGGTATCATTCACAACAACAAATAATAATTTTAATAAAGATGATTCTAACGAGCATGCG
AGTGCCTCATTACTTCAAATTAAAAGGACACTAAAAATAGCAAATATCGAGTTTCAAGAT
AATGCTACAAATTTTAAAACTTCATGTCCAGTTTGTGAAAAATCATATTCTCAACAAAAG
GATATTTATATCAATAAAACAACTGGATATTTCATGTGTCCAAGTTGTAGATATGGTGGT
AAATTAGGATTAATTGAGAAATTCTTTACTACTTCACGATCCCAAAAAATAACCAATGAA
TTGAAAACTTATCAAAAGTTATTTCAAAACGCCAAAGAACAATATCAAAATGAAAATGAA
TTTGATTACCAATTTTATGAAAGAGAATATGAATTAGTGACTGAAGGAAATGCTGATAAT
ATATTTAAACAGTTTTCTATTGATGAAAGGATTTCAAAATCGTCATTAATTGGACTGAAT
AGTAGATATAATCAAGAAAGACAAGAACTTTTATTTCCTCTTATCGACATTATTGGTAAT
ATAGTTGGTTGTAAAATTGTCACAAAATTGAATGACACAGAATGGAAAGAAGTATCTTTA
CCCGATCAAAATGTCTCAGGTGTTATAATTTACAATAATTCAAAAATCAATAAATCAAAA
GACAAAGAACTACCTCAACAAAAGGCGATAGTTGTACTCAATATTCTTGACTTACTTGCA
TTAACAACAACTAAAATTAATGCAGCATTTATTTGTTTACCATATGGACTTAAGTTTCTT
CCTCAAGAGTGTCTTCCTATTCTTGATCAATATAATGAGCTCACACTTTGGTTTAATTAT
AACACTGCAGGCTGGGATGTAGCAAGAAATTTTGCCAAAAAACTTGATGAAAAACGTTGC
AAGTTTGTTAGACCAACTTCTGCTCATCCTACACCTTATAAAGCACTCATACAAAGTATT
GATATAAAAAGCATTTTTTCAAAGTCGACGTCAATTTTACATAAGGCAATTACAACATTT
GCTTCACTACGACAAGATGTTTTGAGTGACTTACAAAACATTGACAAAGTTCAAGGTGTA
AAATGGAAAAGATATCCTACACTCAATAAGTATTTAAAAGGTCATAGAAAAGGTGAACTT
ACAATTTTAACAGGTTCAACAGGTTGTGGAA
>g1838.t2 Gene=g1838 Length=410
MFAHRVLLSNHLTKSFNVLKKVSFTTTNNNFNKDDSNEHASASLLQIKRTLKIANIEFQD
NATNFKTSCPVCEKSYSQQKDIYINKTTGYFMCPSCRYGGKLGLIEKFFTTSRSQKITNE
LKTYQKLFQNAKEQYQNENEFDYQFYEREYELVTEGNADNIFKQFSIDERISKSSLIGLN
SRYNQERQELLFPLIDIIGNIVGCKIVTKLNDTEWKEVSLPDQNVSGVIIYNNSKINKSK
DKELPQQKAIVVLNILDLLALTTTKINAAFICLPYGLKFLPQECLPILDQYNELTLWFNY
NTAGWDVARNFAKKLDEKRCKFVRPTSAHPTPYKALIQSIDIKSIFSKSTSILHKAITTF
ASLRQDVLSDLQNIDKVQGVKWKRYPTLNKYLKGHRKGELTILTGSTGCG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g1838.t2 | Coils | Coil | Coil | 114 | 134 | - |
| 1 | g1838.t2 | PANTHER | PTHR12873:SF0 | TWINKLE PROTEIN, MITOCHONDRIAL | 26 | 410 | 2.5E-49 |
| 2 | g1838.t2 | PANTHER | PTHR12873 | T7-LIKE MITOCHONDRIAL DNA HELICASE | 26 | 410 | 2.5E-49 |
| 3 | g1838.t2 | 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
There are no GO annotations for this transcript.
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