RetrogeneDB ID: | retro_cjac_239 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 15:87805285..87806260(-) | ||
| Located in intron of: | ENSCJAG00000020148 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000020160 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000004677 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_239
ATGATGTCTAGCAACTCCAGTGAAGCTGATGTGATAATAACAAGAATATCTACTTATGATGATGACAACACTGTTCTTCA
TGCATATGAAACAAAACATAAATTTGCAAATGAAACAAAAACTGAGCAGGAACCGATTACTGTAGCTGATGCATCCTGTA
ATACTGAAGAGCAACCGAAGTCAGTGTATGATGTCGTTACCTATTGCCAAGTTATATATGATACTATCCAAAACCTGGAT
AAGAAGATTGATGGCATTAGCAGAAAGGTTTCAAAAATCCAACGTTTCAATGCAAAAGCAGTGTGGACGAATCGCAAGCC
ATCTGGCTTTGGATATGGATATGCATACAGAAATTATTCTTGCCTGCTTGCTAAAAAGCTTAAACTCCAGAAAACGAAGA
AAAGTCAGGCTTACGAGACATTCTCCTACCCTCAAAGTTATAGTCCCACTTCACCAGTGGCAGTGCAGGCGGATAATTCC
CAGAGGAACAATCCAGCACCATCCTTTCACATGGAAGAAGAATACCAGCGAGCTGAGCCGGAGGAGGACCCAGTCCTCAG
CTGCACTCCGAGTCCAGTGCATCCCTCAGACCACTCTGAGCATGGTTTTCAACCATCTTATGCATCTGATGGTGCAATGC
CTGGCTCTTCAGGGCCCTACCGTGGCAGCGCTAGGGTTAACAGCAGCCAAGTTACAAGCATACCAATGGACAATGACCTG
TATTTAGAGGACAACTTCATTAAGCACCCTGCAACATGGTCGGTGGAAGCAGTGGGTTTATTTCTGAAGCAAACGGATCC
TAAGACATTATGCCCTCTTGTCGATCTCTTCAGAACCTATAAAACTGATGGGAAGGCTCTGCTCCTACTCACGAGCGACC
TGATGCTGAAGTACTTGGGTCGGAAGCTGGGAAGGGTCATGAAGCTATGCTACTACATTGAACAACTTAAACAAGGAAAA
TGCTTTGAAAATTAA
ORF - retro_cjac_239 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.07 % |
| Parental protein coverage: | 67.95 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MMSSNTSEADVIKTRISTYDDDNTVVLHAYETKHKFANETKTE-EPITVADASCNTEEQPKSVYDVLTYC |
| MMSSN.SEADVI.TRISTYDDDNTV.LHAYETKHKFANETKTE.EPITVADASCNTEEQPKSVYDV.TYC | |
| Retrocopy | MMSSNSSEADVIITRISTYDDDNTV-LHAYETKHKFANETKTEQEPITVADASCNTEEQPKSVYDVVTYC |
| Parental | QVIYDAIQNLDKKIDGISRKVSKIQRFNAKAGSTNRKPSGFGYGYAYRNYSCLLAKKLKLQKMKKSQAYE |
| QVIYD.IQNLDKKIDGISRKVSKIQRFNAKA..TNRKPSGFGYGYAYRNYSCLLAKKLKLQK.KKSQAYE | |
| Retrocopy | QVIYDTIQNLDKKIDGISRKVSKIQRFNAKAVWTNRKPSGFGYGYAYRNYSCLLAKKLKLQKTKKSQAYE |
| Parental | TFSYSQSYSPTSPVAVRADDSQSNNPAPSFHM-EEYQRAEPEEDPVLSCTPSPVHPSDHSEHGFQPSYAS |
| TFSY.QSYSPTSPVAV.AD.SQ.NNPAPSFHM.EEYQRAEPEEDPVLSCTPSPVHPSDHSEHGFQPSYAS | |
| Retrocopy | TFSYPQSYSPTSPVAVQADNSQRNNPAPSFHMEEEYQRAEPEEDPVLSCTPSPVHPSDHSEHGFQPSYAS |
| Parental | DGAMPGSSRPYRGSTRVNSSQ |
| DGAMPGSS.PYRGS.RVNSSQ | |
| Retrocopy | DGAMPGSSGPYRGSARVNSSQ |
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 .00 RPM | 0 .09 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .09 RPM | 0 .60 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_239 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_239 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_239 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 | ENSCJAG00000004677 | 1 retrocopy |
retro_cjac_239 ,
|
| Vicugna pacos | ENSVPAG00000003425 | 1 retrocopy |