RetrogeneDB ID: | retro_cjac_1425 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 15:87467894..87468677(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDHX | ||
| Ensembl ID: | ENSCJAG00000010888 | ||
| Aliases: | None | ||
| Description: | pyruvate dehydrogenase complex, component X [Source:HGNC Symbol;Acc:21350] |
Retrocopy-Parental alignment summary:
>retro_cjac_1425
ATTGGTTTGATAGAAGAAGAAGATTGGAAACACGTTGAAATTCCCAAAGATGTAGGTCCTCCACCACCAGCTTCAAAACC
TTCAGAGCCTCGTCCCTCACCAGAACCACAGATTGCCATCCCTGTCAAGAAGGAACACACACCCAGGATACTACAGTTCC
GTTTAAGGCCAGCTGCCTGCAATATTCTGGAAGAACACTCACTGGATGCTAACCAGGGCACAGCCAATGGTCCTCGGGGG
ATATTCACAAAAGAGGATGCTCTCAGACTTGCCCAGTTGAAACAGATGGTGGCCAAGATTACCGAGTCCAGATCAACCCC
AGCCCCTGCAGCCACTCCCACAGCACCTTCACCCCTACAGGCCATAACCGGGCCATCTTATCCCCGGCTTATGATCCCAC
CAGCATCCACTCCTGGACAACCCAATGCAGTGGGCACATTCACTGAAATCCCCGCCAGCAATATTCCAAGAGTTATTGCC
AAGAGATTAACTGAATCGAAAAGTACTGTACCTCATGCGTATGCTACTGCTGACTTTGACCTTGGAGCTGTTTTAAAAGT
TAGGCAAGATCTGGTCAAAGGTGACATTAGAGTATCAGTAAATGATTTTATCATCAAGGCAGCAGCTGTTACCCTTAAAC
AAATGCCAGATGTTAAAGTGAGCTGGGATGGAGAGGGCCCAAAGCAACTGCCATGTGTTGACATTTCAGTGGCCGAGGCA
ACAGATAAAGGCTTCATTACACCAGTCATTAAGGATGCTGCTGCTAAGGGTATCCAGGCTCTG
ORF - retro_cjac_1425 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.17 % |
| Parental protein coverage: | 52.1 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | IGLIVEEGEDWKHVEIPKDVGPPPPPSKPSEPRPSPEPQVAIPVKKEHTPGTLQFRLSPAARNILEKHSL |
| IGLI.EE..DWKHVEIPKDVGPPPP.SKPSEPRPSPEPQ.AIPVKKEHTP..LQFRL.PAA.NILE.HSL | |
| Retrocopy | IGLIEEE--DWKHVEIPKDVGPPPPASKPSEPRPSPEPQIAIPVKKEHTPRILQFRLRPAACNILEEHSL |
| Parental | DASQGTATGPRGIFTKEDALRLAQLKQM-GKITESRPAPAPAATPTAPSPLQATAGPSYPRPMIPPVSTP |
| DA.QGTA.GPRGIFTKEDALRLAQLKQM..KITESR..PAPAATPTAPSPLQA..GPSYPR.MIPP.STP | |
| Retrocopy | DANQGTANGPRGIFTKEDALRLAQLKQMVAKITESRSTPAPAATPTAPSPLQAITGPSYPRLMIPPASTP |
| Parental | GQPFAVGTFTEIPASNIRRVIAKRLTESKSTVPHAYATADCDLGAVLKVRQDLVKDDIKVSVNDFIIKAA |
| GQP.AVGTFTEIPASNI.RVIAKRLTESKSTVPHAYATAD.DLGAVLKVRQDLVK.DI.VSVNDFIIKAA | |
| Retrocopy | GQPNAVGTFTEIPASNIPRVIAKRLTESKSTVPHAYATADFDLGAVLKVRQDLVKGDIRVSVNDFIIKAA |
| Parental | AVTLKFLKNILVSWDGEAPKQLPCIDISVV-ATDKGLITPIIKDAAAKGIQEI |
| AVTLK......VSWDGE.PKQLPC.DISV..ATDKG.ITP.IKDAAAKGIQ.. | |
| Retrocopy | AVTLKQMPDVKVSWDGEGPKQLPCVDISVAEATDKGFITPVIKDAAAKGIQAL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .24 RPM | 12 .03 RPM |
| SRP051959_heart | 0 .63 RPM | 31 .15 RPM |
| SRP051959_kidney | 0 .31 RPM | 19 .50 RPM |
| SRP051959_liver | 0 .43 RPM | 15 .57 RPM |
| SRP051959_lung | 0 .29 RPM | 15 .16 RPM |
| SRP051959_lymph_node | 0 .09 RPM | 9 .82 RPM |
| SRP051959_skeletal_muscle | 0 .70 RPM | 28 .17 RPM |
| SRP051959_spleen | 0 .17 RPM | 12 .46 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1425 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1425 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1425 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000003998 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000010888 | 1 retrocopy |
retro_cjac_1425 ,
|
| Mus musculus | ENSMUSG00000010914 | 1 retrocopy |