RetrogeneDB ID: | retro_cjac_285 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286243.1:66195..67377(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000011987 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000000511 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_285
TCCATTTTTGGGGGCACGGATATGAAGAAGGCCATTGCCTGCCTGCTCTTTGGGGGATCCCGAAAGAGGCTCCCTGATGG
ACTTACTCGCCGAGGAGACATCAACCTGCTGATGCTAGGGGACCCTGGGACAGCCAAGTCCCAGCTTCTGAAGTTTGTGG
AGAAGTGTTCTCCCATTGGGGTTTACACGTCTGGGAAAGGGAGCAGTGCAGCCGGACTGACAGCCTCGGTGATGAGGGAC
CCTTCGTCCCGGAATTTCATCATGGAAGGTGGAGCCATGGTCCTGGCTGATGGTGGGGTCGTCTGTATTGATGAGTTTGA
CAAGATGCGAGAAGACGACCGTGTGGCAATCCATGAAGCCATGGAGCAGCAGACCATCTCTATTGCCAAGGCTGGGATCA
CCACCACCCTGAACTCTCGCTGCTCCGTCCTGGCTGCTGCCAACTCAGTGTTTGGCCGCTGGGATGAGACGAAGGGGGAG
GACAACATTGATTTCATGCCTACCATCTTGTCGCGCTTCGATATGATCTTCATTGTCAAGGATGAGCACAATGAGGAGAG
GGATGTGATGCTGGCCAAGCATGTCATTACTCTGCACGTAAGTGCACTGACACAGACACAGGCCGTGGAGGGCGAGATCG
ACCTGGCCAAGCTGAAGAAGTTTATTGCCTACTGCCGAGCGAGGTGCGGCCCCCGGCTGTCAGCAGAGGCCGCAGAGAAG
CTGAAGAACCGCTACATCATCATGCGGAGCGGGGCCCGTCAGCACGAGAGGGACAGTGACCGCCGCTCCAGCATCCCCAT
CACTGTGCGGCAGCTGGAGGCCATTGTGCGAATCGCTGAAGCCCTCAGCAAGATGAAGCTGCAGCCCTTCGCCACAGAGG
CAGATGTGGAGGAGGCCCTGCGGCTCTTCCAAGTGTCCACGTTGGATGCTGCCTTGTCCGGTACCCTGTCAGGGGTGGAG
GGCTTCACCAGCCAGGAGGACCAGGAGATGCTGAGCCGCATCGAGAAGCAGCTCAAGCGCCGCTTTGCCATTGGCTCCCA
GGTGTCTGAGCACAGCATTATCAAGGACTTCACCAAGCAGAAATACCCGGAACATGCCATCCTCAAGGTGCTGCAGCTCA
TGCTGCGGCGGGGCGAGATCCAGCATCGCATGCAGCGCAAAGTTCTCTACCGCCTCAAGTGA
ORF - retro_cjac_285 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.67 % |
| Parental protein coverage: | 53.11 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TLVGGWTGDLAVLTLPISPSFPRLPDGLTRRGDINLLMLGDPGTAKSQLLKFVEKCSPIGVYTSGKGSSA |
| ...GG.....A...L....S..RLPDGLTRRGDINLLMLGDPGTAKSQLLKFVEKCSPIGVYTSGKGSSA | |
| Retrocopy | SIFGGTDMKKAIACLLFGGSRKRLPDGLTRRGDINLLMLGDPGTAKSQLLKFVEKCSPIGVYTSGKGSSA |
| Parental | AGLTASVMRDPSSRNFIMEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSR |
| AGLTASVMRDPSSRNFIMEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSR | |
| Retrocopy | AGLTASVMRDPSSRNFIMEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSR |
| Parental | CSVLAAANSVFGRWDETKGEDNIDFMPTILSRFDMIFIVKDEHNEERDVMLAKHVITLHVSALTQTQAVE |
| CSVLAAANSVFGRWDETKGEDNIDFMPTILSRFDMIFIVKDEHNEERDVMLAKHVITLHVSALTQTQAVE | |
| Retrocopy | CSVLAAANSVFGRWDETKGEDNIDFMPTILSRFDMIFIVKDEHNEERDVMLAKHVITLHVSALTQTQAVE |
| Parental | GEIDLAKLKKFIAYCRARCGPRLSAEAAEKLKNRYIIMRSGARQHERDSDRRSSIPITVRQLEAIVRIAE |
| GEIDLAKLKKFIAYCRARCGPRLSAEAAEKLKNRYIIMRSGARQHERDSDRRSSIPITVRQLEAIVRIAE | |
| Retrocopy | GEIDLAKLKKFIAYCRARCGPRLSAEAAEKLKNRYIIMRSGARQHERDSDRRSSIPITVRQLEAIVRIAE |
| Parental | ALSKMKLQPFATEADVEEALRLFQVSTLDAALSGTLSGVEGFTSQEDQEMLSRIEKQLKRRFAIGSQVSE |
| ALSKMKLQPFATEADVEEALRLFQVSTLDAALSGTLSGVEGFTSQEDQEMLSRIEKQLKRRFAIGSQVSE | |
| Retrocopy | ALSKMKLQPFATEADVEEALRLFQVSTLDAALSGTLSGVEGFTSQEDQEMLSRIEKQLKRRFAIGSQVSE |
| Parental | HSIIKDFTKQKYPEHAILKVLQLMLRRGEIQHRMQRKVLYRLK |
| HSIIKDFTKQKYPEHAILKVLQLMLRRGEIQHRMQRKVLYRLK | |
| Retrocopy | HSIIKDFTKQKYPEHAILKVLQLMLRRGEIQHRMQRKVLYRLK |
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 .04 RPM | 4 .06 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .25 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .33 RPM |
| SRP051959_liver | 0 .02 RPM | 1 .21 RPM |
| SRP051959_lung | 0 .00 RPM | 1 .35 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .83 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .24 RPM |
| SRP051959_spleen | 0 .02 RPM | 4 .41 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_285 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_285 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_285 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000000511 | 1 retrocopy |
retro_cjac_285 ,
|
| Myotis lucifugus | ENSMLUG00000001987 | 1 retrocopy |