RetrogeneDB ID: | retro_cjac_976 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 12:41077909..41078651(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | WDR85 | ||
| Ensembl ID: | ENSCJAG00000013422 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_976
GCCTTCAATTGCTGGCATACAGAAATTATATATTCAGGGGGTGATGACTACTGGCCTACTGAGGGGCTGAGACAACAGGG
AACCTGGCAGATTTCTCTTCACCATCAAGAGATACTCCATGGGTGTGTGCAGTATCCAGAGCAGCCCCCATCGAGAGCAT
GTCCTGGCCACAGGAAGCTATGATGAGCACATCCTACTGTGGGATATATGAAACATGAAGCAATCATTGGCAGACACACC
TGTGCAGGGTGGGGTATGGAGAATCAAGTGGCACCCTTTCCACCACCACCTGCTTCTGGTCGCCTGTATGCACAGTGGCT
GTAAGATCCTCAACTGCCCAAAGGCAATGGAGGAGAAGCAGGAGGCGACGGTCCTGGCATATCACACATTGCCTAACTTG
CTGGTGTACGGAGCCGACTGGTCATAGCTGCTCTTTCATTCTCTGCAACTGGCCCTCTCGCGGCCCTGTCCTAGCAACCT
GGGAACCAAGACAGCAGACCTGAAGGGTACAAGCAAGTTGTCAGCACCCTGTCGTGAATGCATGGAGGATAATGATGGAG
AGGGCTGGGGAGTGAAGCCACTCACAGAGGACATGAGGAGGAATGGCACCTGGCTGTGGGCTACAGCAGCTGCCAAGCGT
GACTGTGGCCTGAGCCCAGAAGAAGCAGACTCAGCCTTCAGCCTCCTAGCCACCTGCTCTTTCTATCAGCATGCGCCCCA
CCTCTGGGAGTGGGAGGGGAGC
ORF - retro_cjac_976 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.66 % |
| Parental protein coverage: | 55.03 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AFNYWHTEIVYS-GGD-DGLLRGWDTRAPGRFLFTSMSHCPGVCSIQSSPHREHVLATGSYDEHILLWDT |
| AFN.WHTEI.YS.G.D..GLLRG.D.R.PGRFLFT......GVCSIQSSPHREHVLATGSYDEHILLWD. | |
| Retrocopy | AFNCWHTEIIYSGGDD>TGLLRG*DNREPGRFLFTIKRYSMGVCSIQSSPHREHVLATGSYDEHILLWDI |
| Parental | RNMKQPLADTPVQGGVWRIKWHPFHHHLLLAACMHSGFKILNCQKAMEEKQEATVLASHTLPNSLVYGAD |
| .NMKQ.LADTPVQGGVWRIKWHPFHHHLLL.ACMHSG.KILNC.KAMEEKQEATVLA.HTLPN.LVYGAD | |
| Retrocopy | *NMKQSLADTPVQGGVWRIKWHPFHHHLLLVACMHSGCKILNCPKAMEEKQEATVLAYHTLPNLLVYGAD |
| Parental | WSWLLFHSLQLAPSRPCPSNLGTKTADLKGASELPGPSCECMEDNDGEGYGVKPLTEDSRENGTWLQATA |
| WS.LLFHSLQLA.SRPCPSNLGTKTADLKG.S.L..P..ECMEDNDGEG.GVKPLTED.R.NGTWL.ATA | |
| Retrocopy | WS*LLFHSLQLALSRPCPSNLGTKTADLKGTSKLSAPCRECMEDNDGEGWGVKPLTEDMRRNGTWLWATA |
| Parental | TTMRDCGQSPEEANSAFSLLATCSFYDHALHLWEWEGN |
| ...RDCG.SPEEA.SAFSLLATCSFY.HA.HLWEWEG. | |
| Retrocopy | AAKRDCGLSPEEADSAFSLLATCSFYQHAPHLWEWEGS |
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 | 3 .53 RPM |
| SRP051959_heart | 0 .00 RPM | 4 .17 RPM |
| SRP051959_kidney | 0 .00 RPM | 4 .30 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .92 RPM |
| SRP051959_lung | 0 .00 RPM | 4 .41 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .82 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 6 .07 RPM |
| SRP051959_spleen | 0 .00 RPM | 4 .37 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_976 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_976 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_976 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 | ENSCJAG00000013422 | 1 retrocopy |
retro_cjac_976 ,
|