RetrogeneDB ID: | retro_mmul_246 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 14:93532010..93533582(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMMUG00000023376 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KDM4B | ||
| Ensembl ID: | ENSMMUG00000012677 | ||
| Aliases: | KDM4B, JMJD2B | ||
| Description: | lysine-specific demethylase 4B [Source:RefSeq peptide;Acc:NP_001253377] |
Retrocopy-Parental alignment summary:
>retro_mmul_246
ATGGAAACTATGAAGTCTAAGGCCAACTATGGCCAGAATCCAAATTGTAACATAATGATATTTCATCCAACCAAAGAAGA
GTTTAATGATTTTGATAAATATATTGCTTACATGGAATCCCAAGGTGCACACAGAGCTGGCTTGGCTAAGATAGTTCCAC
CCAAAGAATGGAAAGCCAGAGAGACCTATGATAACATCAGTGAAATCTTAATAGCCACTCCCCTCCAACAGGTGGCCTCT
GGGCGGGCAGGGGTGTTTACTCAATACCATAAAAAAAAGAAAGCCATGACCGTGGGGGAGTATCGCCACTTGGCAAACAG
TAAAAAATATCAAACTCCACCACACCAGAATTTCGAAGATTTGGAGCGAAAATACTGGAAGAACCGCATCTATAATTCAC
CAATTTATGGTGCTGACATCAGTGGCTCCTTGTTTGATGAAAACACTAAACAGTGGAATCTTGGGCACCTGGGAACAATT
CAGGACCTGTTGGAAAAGGAATGTGGGGTTGTCATAGAAGGCGTTAACACACCCTACTTGTACTTTGGCATGTGGAAGAC
CACATTTGCTTGGCACACGGAGGACATGGACCTTTACAGCATCAACTACCTGCACCTCGGGGAGCCCAAAACTTGGTATG
TGGTGCCCCCAGAGCATGGCCAGCGCCTGGAACGCCTGGCCAGGGAGCTCTTCCCAGGCAGTTCCCGGGGCTGTGGGGCC
TTCCTGCGGCACAAGGTGGCCCTCATCTCGCCTACAGTTCTCAAGGAAAATGGGATCCCCTTCAATCGCATAACTCAGGA
GGCTGGAGAGTTCATGGTGACCTTTCCCTATGGCTACCATGCTGGCTTCAACCATGGTTTCAACTGTGCAGAGGCCATCA
ATTTTGCCACTCCACGATGGATTGATTATGGCAAAATGGCCTCCCAGTGTAGCTGTGGGGAGGCCAGGGTGACCTTTTCC
ATGGACGCCTTCGTGCGCATCCTGCAACCTGAGCGCTATGAGCTGTGGAAACGTGGGCAAGACCGGGCAGTTGTGGACCA
CATGGAGCCCAGGGTACCAGCCAGCCAAGAGCTGAGCACCCAGAAGGAGGTCCAGTTGCCCAGGAGAGCAGCGCTGGGCC
TGAGACAACTCCCTCCTCACTGGGCCCGGCATTCCCCTTGGCCTCTGGCTGCCCGCAGTGGGACGCGCTGCCACACCCTT
GTGTGCTCTTCACTCCCACGCCGATCTGCAGTTAGTGGCACTGCTACGCAGCCCCGGGCTGCTGCCGTCCACAGCTCTAG
GAAGCCCAGCTCAACTCCATCATCCACCCCTGGTCCATCTGCACAGATTATCCACCCGTCAAATGGCAGACGTGGACGTG
GTCGCCGTCCTCAGAAACTGAGAGCTCAGGAGCTGACCCTCCAGACTCCAGCCAAGAGGCTCCTCTTAGCGGGCACAACA
TGCACAGTTTCAGGCCCAGAACCTGAGCCCCTACCTGAGGGTGGGGCTTTGATGGACAAGCCTGTACCACTGAATCCAGG
GCTCCAGCATCCTGTAAAGGCTTCTAGGTGCAGCTGGGCCCCTGTGCCCTAA
ORF - retro_mmul_246 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.51 % |
| Parental protein coverage: | 87.31 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MGSEDHGAQNPSCKIMTFRPTMEEFKDFNKYVAYIESQGAHRAGLAKIIPPKEWKPRQTYDDIDDVVIPA |
| M.S.....QNP.C.IM.F.PT.EEF.DF.KY.AY.ESQGAHRAGLAKI.PPKEWK.R.TYD.I....I.. | |
| Retrocopy | MKSKANYGQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIVPPKEWKARETYDNISEILIAT |
| Parental | PIQQVVTGQSGLFTQYNIQKKAMTVGEYRRLANSEKYCTPRHQDFDDLERKYWKNLTFVSPIYGADISGS |
| P.QQV..G..G.FTQY...KKAMTVGEYR.LANS.KY.TP.HQ.F.DLERKYWKN....SPIYGADISGS | |
| Retrocopy | PLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGS |
| Parental | LYDDDVAQWNIGSLRTILDMVERECGTIIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWY |
| L.D....QWN.G.L.TI.D..E.ECG..IEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLH.GEPK.WY | |
| Retrocopy | LFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWY |
| Parental | AIPPEHGKRLERLAIGFFPGSSQGCDAFLRHKMTLISPIILKKYGIPFSRITQEAGEFMITFPYGYHAGF |
| ..PPEHG.RLERLA...FPGSS.GC.AFLRHK..LISP..LK..GIPF.RITQEAGEFM.TFPYGYHAGF | |
| Retrocopy | VVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGF |
| Parental | NHGFNCAESTNFATLRWIDYGKVATQCTCRKDMVKISMDVFVRILQPERYELWKQGKDLTVLDHTRPTAL |
| NHGFNCAE..NFAT.RWIDYGK.A.QC.C....V..SMD.FVRILQPERYELWK.G.D..V.DH..P... | |
| Retrocopy | NHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYELWKRGQDRAVVDHMEPRVP |
| Parental | TSPELSSWSASRASLKAKL-LRR-TPFCASVSPLPHRPQPGVWC |
| .S.ELS..........A.L.LR...P..A..SP.P.....G..C | |
| Retrocopy | ASQELSTQKEVQLPRRAALGLRQLPPHWARHSPWPLAARSGTRC |
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 .45 RPM | 19 .27 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .71 RPM | 62 .04 RPM |
| SRP007412_cerebellum | 1 .03 RPM | 23 .12 RPM |
| SRP007412_heart | 0 .65 RPM | 21 .02 RPM |
| SRP007412_kidney | 0 .23 RPM | 19 .72 RPM |
| SRP007412_liver | 0 .28 RPM | 23 .20 RPM |
| SRP007412_testis | 218 .28 RPM | 25 .03 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_246 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_246 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_246 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 | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000012677 | 1 retrocopy |
retro_mmul_246 ,
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