RetrogeneDB ID: | retro_cjac_391 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:29561382..29561781(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | CD320 | ||
| Ensembl ID: | ENSCJAG00000010700 | ||
| Aliases: | None | ||
| Description: | CD320 molecule [Source:HGNC Symbol;Acc:16692] |
Retrocopy-Parental alignment summary:
>retro_cjac_391
CAGAACGGGCAATGCCCACTGCCCCCTGATTTCCCCTGCTCCTGCACTGGAGTCAGTGACTGCTCCGGGGAAACTGACGA
GAATCTGCGCAATTGCAGCCACCCAGCCTGCCCAGCAGAAGAGCTCGTTGCACGCTGAGTAATGAATGCATTCCACTCAC
GTGGCTCTGCGATGGCCACCCAGACTGTTCCAACTCCAGTGACGAGCTCAGCTGTGGAACCAGGGAGACCCTCTTGGAAG
GGAATGCCACAATCTTGAGGCCCCCTGTGACCTTGGAGGGTGTCATTTCTCGGAAATGCAACGTCCTCCTTCTGAAGACC
AAGTGCCTATGGGGTTATTGTAGTTGCTGCCTTGCTGAGTACAAGCCTGGTGGTCACAACCCTCCTCCTTTTGTTCTGG
CAGAACGGGCAATGCCCACTGCCCCCTGATTTCCCCTGCTCCTGCACTGGAGTCAGTGACTGCTCCGGGGAAACTGACGA
GAATCTGCGCAATTGCAGCCACCCAGCCTGCCCAGCAGAAGAGCTCGTTGCACGCTGAGTAATGAATGCATTCCACTCAC
GTGGCTCTGCGATGGCCACCCAGACTGTTCCAACTCCAGTGACGAGCTCAGCTGTGGAACCAGGGAGACCCTCTTGGAAG
GGAATGCCACAATCTTGAGGCCCCCTGTGACCTTGGAGGGTGTCATTTCTCGGAAATGCAACGTCCTCCTTCTGAAGACC
AAGTGCCTATGGGGTTATTGTAGTTGCTGCCTTGCTGAGTACAAGCCTGGTGGTCACAACCCTCCTCCTTTTGTTCTGG
ORF - retro_cjac_391 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.56 % |
| Parental protein coverage: | 51.75 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | QNGQCPPPPGHLCSCTGVSDCSGETDEKLRNCSRPTCPAGEL-HCTLSDECIPLTWLCDGHPDCSDSSDE |
| QNGQCP.PP...CSCTGVSDCSGETDE.LRNCS.P.CPA.EL..CTLS.ECIPLTWLCDGHPDCS.SSDE | |
| Retrocopy | QNGQCPLPPDFPCSCTGVSDCSGETDENLRNCSHPACPAEEL<RCTLSNECIPLTWLCDGHPDCSNSSDE |
| Parental | LGCGTSETLLKGNATTMGPPVTFESVTSLR-NATSSGRPSAYGVIAVAAVLSTSLVAATLLLLFW |
| L.CGT.ETLL.GNAT...PPVT.E.V.S......S..RPSAYGVI.VAA.LSTSLV..TLLLLFW | |
| Retrocopy | LSCGTRETLLEGNATILRPPVTLEGVISRK>ATSSF*RPSAYGVIVVAALLSTSLVVTTLLLLFW |
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 .02 RPM | 6 .74 RPM |
| SRP051959_heart | 0 .04 RPM | 6 .28 RPM |
| SRP051959_kidney | 0 .02 RPM | 23 .47 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .59 RPM |
| SRP051959_lung | 0 .02 RPM | 2 .10 RPM |
| SRP051959_lymph_node | 0 .09 RPM | 3 .10 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .89 RPM |
| SRP051959_spleen | 0 .06 RPM | 2 .63 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_391 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_391 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_391 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000010700 | 1 retrocopy |
retro_cjac_391 ,
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