RetrogeneDB ID: | retro_mmul_686 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 1099214579365:141..636(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MMU.19027 | ||
| Ensembl ID: | ENSMMUG00000022932 | ||
| Aliases: | None | ||
| Description: | trafficking protein particle complex subunit 6A [Source:RefSeq peptide;Acc:NP_001181407] |
Retrocopy-Parental alignment summary:
>retro_mmul_686
GGGGCATGAGGCTAACACATGGTAGATGCTGTGCTGTTCGAGTTTCTACACACGGAGATGGTAGCAGAGCTGTGGCATCA
CAAATCCAACCCTGTCCGGTGGGGAGGGGAACAGAAGATAAGCCTGTTGATCCTGGAGAGCATGGATTTCTGTGTGAGCC
AGGTTCTAGGCAAGAGACTGCCCCTGGAGATGCTCATCTCAGGGAGGAGCTGGGTGTCCTCAAGTTCATATGCAAAAATC
TGTGGGTGACTGTGTTCCAACAGATGGACAGCCCGTGCACCAATCACCAAGGGACCTACTTTTTTCAGGACAACAGCTTC
CACTCCTCATCCCGATGATCTTGGGCCTGCAGTATCTGGAGGAAGCACCCAAGTTCCTGGATTCACTTGTGGCCTCCTGC
GTGGCACCCTCAGTACCCTGGGCATACAGAGTTTGGTCACTGCCTCCGTGGCAACCCTGATCACCTGTAAGTTCCCACTG
ATACTCTGGAAATCC
ORF - retro_mmul_686 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.88 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | GARGGLMADTVLFEFLHTEMVAELWAHDPDP--GPGGQKMSLSVLESMGFRVGQALGERLPRETLA-FRE |
| GA.G..M.D.VLFEFLHTEMVAELW.H...P....G.QK.SL..LESM.F.V.Q.LG.RLP.E.L...RE | |
| Retrocopy | GA*G*HMVDAVLFEFLHTEMVAELWHHKSNPVRWGGEQKISLLILESMDFCVSQVLGKRLPLEMLI<LRE |
| Parental | ELDVLKFLCKDLWVAVFQKQMDSLRTNHQGTYVLQDN-LPPPPSDGLWPAVSGGSAQVPGL-CGLLRGAL |
| EL.VLKF.CK.LWV.VFQ.QMDS..TNHQGTY..QDN....P..D.L.PAVSGGS.QVPG..CGLLRG.L | |
| Retrocopy | ELGVLKFICKNLWVTVFQ-QMDSPCTNHQGTYFFQDN>ASTPHPDDLGPAVSGGSTQVPGFTCGLLRGTL |
| Parental | CTLGIESVVTASVAALPVCKFQVLIPKS |
| .TLGI.S.VTASVA.L..CKF.....KS | |
| Retrocopy | STLGIQSLVTASVATLITCKFPLILWKS |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 1 .23 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 5 .39 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 1 .94 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .47 RPM |
| SRP007412_kidney | 0 .00 RPM | 3 .87 RPM |
| SRP007412_liver | 0 .00 RPM | 5 .19 RPM |
| SRP007412_testis | 0 .00 RPM | 5 .80 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_686 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_686 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_686 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012869 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000022932 | 1 retrocopy |
retro_mmul_686 ,
|
| Pongo abelii | ENSPPYG00000010109 | 1 retrocopy |