General information for g11425.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mitochondrial proton/calcium exchanger protein.
Parent gene
- The parent gene g11425 is located on chr_1: 16158319..16159180 (- 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 | g11425 | g11425.t1 | TTS | g11425.t1 | 16155617 | 16155617 |
| chr_1 | g11425 | g11425.t1 | isoform | g11425.t1 | 16155734 | 16158968 |
| chr_1 | g11425 | g11425.t1 | exon | g11425.t1.exon1 | 16155734 | 16155859 |
| chr_1 | g11425 | g11425.t1 | cds | g11425.t1.CDS1 | 16155734 | 16155859 |
| chr_1 | g11425 | g11425.t1 | exon | g11425.t1.exon2 | 16155914 | 16156159 |
| chr_1 | g11425 | g11425.t1 | cds | g11425.t1.CDS2 | 16155914 | 16156159 |
| chr_1 | g11425 | g11425.t1 | exon | g11425.t1.exon3 | 16156215 | 16156319 |
| chr_1 | g11425 | g11425.t1 | cds | g11425.t1.CDS3 | 16156215 | 16156319 |
| chr_1 | g11425 | g11425.t1 | exon | g11425.t1.exon4 | 16156386 | 16158340 |
| chr_1 | g11425 | g11425.t1 | cds | g11425.t1.CDS4 | 16156386 | 16158340 |
| chr_1 | g11425 | g11425.t1 | exon | g11425.t1.exon5 | 16158908 | 16158968 |
| chr_1 | g11425 | g11425.t1 | cds | g11425.t1.CDS5 | 16158908 | 16158968 |
| chr_1 | g11425 | g11425.t1 | TSS | g11425.t1 | 16159218 | 16159218 |
Sequences
>g11425.t1 Gene=g11425 Length=2493
ATGAAGGCACTATTAAGTCATCATAAAACATTATTAAGGATTAAAAGCTATAAAATAAAT
GCTAAAAGCTTATCGTCGAAGTATTCAAACATACACATCTCGCCCATACATCTTGAAGTG
ACAAATAATGCAAATAGCCTCAAGTATTGGAAAACACAATATTGTCCATACAATGCAACT
TATCGGCGGTCTATCTTCACATCAAGCTCATGCTTGGAAAAATCTTCTTCTAAAATTGAA
GATGCAGTGAAAACATTAAAAGAAGCTGAAAAAGAAAAGGAAAAGATTATTGAAGGAAAA
AGTACAGTTGTAGGAACTAGCCACGAATCGATAGATTCATCTAAAGCACAAGAAAATATT
ATAAACACTTCAAGTTCCCAACATTTAACGGAACAAAAAATGCAAAAAACAACGGAAGTT
GTCCCAATAGTACCTGTCAAGAAGACAATGTTGCAAAAAATATGGGCTGAACTTGTACAT
TATTATCACGGTTTTAGATTGCTTTTCATTGACATTAACATTTCTCGAAAGTTACTATGG
AAAGTTCTCAATGGAGGAACTCTATCAAGGAGGGAACATCGGTTAATGATTAGAACGACA
TCAGATCTTTTTCGACTTGTGCCATTTTCGGTTTTTATTATTGTTCCATTTATGGAATTG
CTTTTACCATTAGCCATCAAGTTTTTCCCTGGCATGTTACCTTCAACTTTTCAAACAGCT
TCTGAAGAGGAAAGAAAAATAAAACAAAATCTAAAAGTAAAGATTGAGATGGCAAAGTTT
TTACAGAAAACTCTCGATGAAATGACAGTTCAACATAAAAATCATCGTTCTGAAGCAGCA
AAAGAATTTTCTGAATTCTTTCAAAGAGTAAGAACATCAGGGACTTTTGCATCGTCTGAT
GAAATTATGAAATTTGCAAAACTTTTTGAAGATGAACTTACATTAGACGCACTTAATCGT
CAACAATTACTTGCACTTTGTCGTGTGCTCGAAGTGAGTACGATAGGAACAACAAATATA
CTTAGATTTCAATTACATATGAAACTAAGAAATTTGGCTGCCGATGATCGAATGATTCAA
AGAGAAGGAATAGATTCATTAAATTTGGCAGAATTGCAACATGCATGTAGATCGCGTGGT
ATGAGAGCGTATGGTATTCCTGAAGATAAACTTAAAATTCAACTTGCGGATTGGATTAAT
CTAAGTCTCAATGAGAAAGTTCCTCCATCATTATTATTATTATCTAGAGCTTTAATGCTG
CCAGAAGATGCCGAAGTTAGTGAAAAACTAAAAGCCACTATGGCAAGTTTACCTGAAACT
ATAGCAACACAAACTAAAGCTGTCATTGGAGAGCGAGAAGGAAAAATTGATAATAAAACA
AAGATTGAAATTCTTAAAGAAGAGCAACGTAGAATTAAAGAAGAAGAAGAAGAAAGGAAA
GAAGCAGAGGCAGAAATTAAGGCTAAAGAGGAGCAACAGCAACAGGCAAAGGCATCAGAA
GAATTGTTACAAGATAAGGCTCCTATTATTCAATCCGATACAATAGTTAAACCTGATCAA
ATAACTGTTAGTTCTCAAGAACCTAAAGAGAGAGTATTACCAAAAATAGAAAAAGAATTG
ACTTCAGAAGACTTGAAAATACTCACGGATGCTTTAAATGAAATCAGTAGTGAGAAAAAA
TTATTATTGGCAAAAGAAGAAATTAAGGAAATTAAAGAAGAAATCGCAGAATATGAGGAG
GATGTCGAAGAGCTCAATAAAATTGTTGAACAAAAGCTTGAAAAGATACAACTGAAAGAA
TCACGTGCAGCTAAATTGCTTCTCAAAAAAGTCAATTCTATGATTAGTAATTTAGATAAA
GCTCTTGAAGATTTAGAGACAAAAGAGAAACAAATTAAAACATTAAATACTGAACCAAGT
AAAGCAACTGAAGCTGTTGATGCAGTTATTGCAGAAGAAGCAAAGCGTACAGAAGAACTT
GTTCGTATTGATGAGATGATGAATGCCATTAGAAAGATACAAAAAGTTTCTGATGAGTCT
GTACTGGAGCAAATTGAAAAGTTGTTGTCAAGAATCGATGATGATCGTGATGGTTCACTG
AAAGTAGAAGATGTTTTAAAGATTATTGAAACTATTGGAAAGGAGAATATCAATTTAAAT
GAGAAGCAAATTAACGAAATAATTGACTTGATTGATAAAGAGGAAATAATTGAAACCGAA
GAAATGATTGAAAAAGCATTAAAAAAAGAACAAGAACAGCGTAATGTATTGAAGAAAGCA
AATGAAGATGATTTCACAACTAGTGAAGTTAATTTTATTTTGCAAGACAAAGCAACAGAA
ATCCAAGAACCATCATCAACAGAAAAGGAAGAAGTTGATGAGAAAATTGTAAAAGCAAAT
AATCAGACGGTCAATGGTGTTGTTGATTCAACAACTACTCTTCCAAAGAAATCTGTTGAG
AGTCCACAGGACACAAAAAACAAAAGTGTGTGA
>g11425.t1 Gene=g11425 Length=830
MKALLSHHKTLLRIKSYKINAKSLSSKYSNIHISPIHLEVTNNANSLKYWKTQYCPYNAT
YRRSIFTSSSCLEKSSSKIEDAVKTLKEAEKEKEKIIEGKSTVVGTSHESIDSSKAQENI
INTSSSQHLTEQKMQKTTEVVPIVPVKKTMLQKIWAELVHYYHGFRLLFIDINISRKLLW
KVLNGGTLSRREHRLMIRTTSDLFRLVPFSVFIIVPFMELLLPLAIKFFPGMLPSTFQTA
SEEERKIKQNLKVKIEMAKFLQKTLDEMTVQHKNHRSEAAKEFSEFFQRVRTSGTFASSD
EIMKFAKLFEDELTLDALNRQQLLALCRVLEVSTIGTTNILRFQLHMKLRNLAADDRMIQ
REGIDSLNLAELQHACRSRGMRAYGIPEDKLKIQLADWINLSLNEKVPPSLLLLSRALML
PEDAEVSEKLKATMASLPETIATQTKAVIGEREGKIDNKTKIEILKEEQRRIKEEEEERK
EAEAEIKAKEEQQQQAKASEELLQDKAPIIQSDTIVKPDQITVSSQEPKERVLPKIEKEL
TSEDLKILTDALNEISSEKKLLLAKEEIKEIKEEIAEYEEDVEELNKIVEQKLEKIQLKE
SRAAKLLLKKVNSMISNLDKALEDLETKEKQIKTLNTEPSKATEAVDAVIAEEAKRTEEL
VRIDEMMNAIRKIQKVSDESVLEQIEKLLSRIDDDRDGSLKVEDVLKIIETIGKENINLN
EKQINEIIDLIDKEEIIETEEMIEKALKKEQEQRNVLKKANEDDFTTSEVNFILQDKATE
IQEPSSTEKEEVDEKIVKANNQTVNGVVDSTTTLPKKSVESPQDTKNKSV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11425.t1 | Coils | Coil | Coil | 72 | 99 | - |
| 7 | g11425.t1 | Coils | Coil | Coil | 258 | 278 | - |
| 6 | g11425.t1 | Coils | Coil | Coil | 458 | 506 | - |
| 5 | g11425.t1 | Coils | Coil | Coil | 561 | 602 | - |
| 10 | g11425.t1 | Coils | Coil | Coil | 608 | 638 | - |
| 9 | g11425.t1 | Coils | Coil | Coil | 733 | 763 | - |
| 15 | g11425.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 800 | 820 | - |
| 16 | g11425.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 800 | 830 | - |
| 2 | g11425.t1 | PANTHER | PTHR14009:SF8 | MITOCHONDRIAL PROTON/CALCIUM EXCHANGER PROTEIN | 28 | 744 | 2.2E-162 |
| 3 | g11425.t1 | PANTHER | PTHR14009 | LEUCINE ZIPPER-EF-HAND CONTAINING TRANSMEMBRANE PROTEIN | 28 | 744 | 2.2E-162 |
| 1 | g11425.t1 | Pfam | PF07766 | LETM1-like protein | 151 | 415 | 4.8E-101 |
| 11 | g11425.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 202 | - |
| 13 | g11425.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 226 | - |
| 12 | g11425.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 227 | 830 | - |
| 17 | g11425.t1 | ProSiteProfiles | PS51758 | Letm1 ribosome-binding (RBD) domain profile. | 249 | 515 | 29.202 |
| 18 | g11425.t1 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 680 | 715 | 9.827 |
| 4 | g11425.t1 | SUPERFAMILY | SSF47473 | EF-hand | 657 | 750 | 4.61E-7 |
| 14 | g11425.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 225 | - |
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:0043022 | ribosome binding | MF |
| GO:0005509 | calcium ion binding | MF |
| GO:0005743 | mitochondrial inner membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K17800 (LETM1 and EF-hand domain-containing protein 1, mitochondrial)
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.
