RetrogeneDB ID: | retro_cjac_1822 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:89922593..89923127(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000016842 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MFAP2 | ||
| Ensembl ID: | ENSCJAG00000008038 | ||
| Aliases: | None | ||
| Description: | microfibrillar-associated protein 2 [Source:HGNC Symbol;Acc:7033] |
Retrocopy-Parental alignment summary:
>retro_cjac_1822
ATGAGAGCTGCCTACCTCTTCCTGCTATTCCTGCCTGCAGGCCCGCTGGTTCAGGGGCAGTATGACCTGGGCCTGCCGCC
GCCATTCCCTGACCATGTCCAGTACACCCACTACGGCGACCAGATCGACAACCCAGACTACTATGATTATCAAGAGGTGA
ATTCTCAGCCTTCGGAGGAACAGTTCCAGTTCCCGTCCCACAGCAAGTCCAACAGGAAGTCATAGCAGCCCCAACCCCAG
AACCAGGAAATGGCAGAGCTGGAGCCCACGGAGCCCAGACCTCTGGACTGCGGTGTGGAGCAGTACCCGTGCACCCGCCT
CTACTCCATACACAAGGCTTGCAAGCAGTGTCTGAACGAGATCTGCTTCTACAGCCACCCCCGCGTGTATGTCATCAATA
AGGAGATCTGTGTCCGCACAGTGTGTGCCCACGAGGAGCTCCTCCAAGCTGACCCCAAGTTCTCCAAATGTGGCGTCATG
GTCAGCAGCGGCCTGTGTCAATCCGTGGCAGCCTCCTGCACCAGGAGCTGTGGG
ORF - retro_cjac_1822 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.89 % |
| Parental protein coverage: | 98.91 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MKAAYLFLLFLPAGPLVQGQYDLDPPPPFPDHVQYTHYGDQIDNPDYYDYQEVTSRPSEEQFQFQSQ-QQ |
| M.AAYLFLLFLPAGPLVQGQYDL..PPPFPDHVQYTHYGDQIDNPDYYDYQEV.S.PSEEQFQF.S..QQ | |
| Retrocopy | MRAAYLFLLFLPAGPLVQGQYDLGLPPPFPDHVQYTHYGDQIDNPDYYDYQEVNSQPSEEQFQFPSH<QQ |
| Parental | VQQEVIAAPTPEPGN-AELEPTEPGPLDCREEQYPCTRLYSIHKPCKQCLNEVCFYSLRRVYVINKEICV |
| VQQEVIAAPTPEPGN.AELEPTEP.PLDC..EQYPCTRLYSIHK.CKQCLNE.CFYS..RVYVINKEICV | |
| Retrocopy | VQQEVIAAPTPEPGN>AELEPTEPRPLDCGVEQYPCTRLYSIHKACKQCLNEICFYSHPRVYVINKEICV |
| Parental | RTVCAHEELLRADLCRDKFSKCGVMASSGLCPSVAASCARSCG |
| RTVCAHEELL.AD....KFSKCGVM.SSGLC.SVAASC.RSCG | |
| Retrocopy | RTVCAHEELLQAD---PKFSKCGVMVSSGLCQSVAASCTRSCG |
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 | 1 .40 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .86 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .29 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .11 RPM |
| SRP051959_lung | 0 .00 RPM | 1 .07 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .14 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .11 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .29 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1822 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1822 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1822 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 | ENSCJAG00000008038 | 1 retrocopy |
retro_cjac_1822 ,
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