RetrogeneDB ID: | retro_mmul_1085 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 14:113047650..113048925(+) | ||
| Located in intron of: | ENSMMUG00000012267 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MMU.10126 | ||
| Ensembl ID: | ENSMMUG00000009948 | ||
| Aliases: | None | ||
| Description: | Histone deacetylase [Source:UniProtKB/TrEMBL;Acc:F6RIU8] |
Retrocopy-Parental alignment summary:
>retro_mmul_1085
CCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCACAGTGATTACTGCATTAAATTATTGTGCTCCATCTGTCCAGA
TTACGTGTCCAAGCACAGCAAGCAGATGCGGGGATTTAATGTTAGTGAGGACTGTCCAGTATCTGATGGCCTGTTTGACT
TCTGTCAGTTGTCTACTGGTGGCTCTGTGGCAAGTGCTGTGAAACTTAATAAGCAGCAGATGGACATTGCTGTGAATTGG
GCTGGGGGCCTGCACCATGCAAAGAAGTTCAAGGCATCTGGCTTCTGTTATATCAGTGATACAATCTGGGCCACCCTGGA
ACTGCTAAAGTATCACCAGAGGGTGTTGTATGTTGATGTTGATATTCACCATGATGATGGCATGGAAGAGACCTTCTATA
TTACAGGCCAGGTCAGGACTGTGTCCTTTCATAAATATGGAGAGTACTTCCCAGGAAATGGGGACCTATGGGATATTGGG
ACTGGCAAGGCAGATATTATGCTGTTAACTGTCTGCTCCTAGATGGGATTGATTATGAGTCCTGTGAGGCCATTTTGAAA
CTGGTCATGTCCAAAGTAATAGAGATGCTCCTGTCTAGCGTGATGGTCTTATGGCATGTCTCAGATGCCTTGTTTAGGGA
TCAGTTAGATTGCTTTAATCTGACCATGAAAGCGCATGCCAAGTGTATGGAATTTGTCAAGAGCTTCAACCTGCCTATAC
TGTTGATGGCAGAAGGTGGTTACACCATTTATAACGTTGCTCAGTGCTGGAAATAAGAAATAGCTGTGGCTCTGGATATG
GAGACTTCTAATGAGCCTTCATACAATGACTAGTTTGAATACTTCAGACCATATTTCAAGCCCTACATCAGTCCTTCCAA
TATGACTAACTAGAACACTAATGAGTACCTGGAGAAGATTAAATAATGGCTGTTTGAGAACCTAGTGATGCAGCCCCATC
CATCTGCAGTCCAAATGCAGGTGATTCCTGAGGATGCTGTCCCTCAAGAGGGTGGCATTGAGAATGAAGAAGACCCTGAC
AAGCATCTCCATCTGTTTCTCTGACAGACGAATTACCTGTGAGGAAGAGTTCTTCGGTTCTGATGAGGAGGGAGAGGGTG
GCCGCAAGATCTCTCCCATCTTCAGAAAATCCAAGAGGGTTAAAACAGGATGAAAAAGAGAGACTCAGAGATGAAGAAAG
AAGTCACAGAAGCGGAGAAAAACAAAGGAGAAGAAGCCAGGAGCCAAAGAGGTCAAGGACCAGGTCAAGCTGGCC
ORF - retro_mmul_1085 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.76 % |
| Parental protein coverage: | 99.77 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLN |
| PHKANAEEMTKYHSD..IK.L.SI.PD..S..SKQM..FNV.EDCPV.DGLF.FCQLSTGGSVASAVKLN | |
| Retrocopy | PHKANAEEMTKYHSDYCIKLLCSICPDYVSKHSKQMRGFNVSEDCPVSDGLFDFCQLSTGGSVASAVKLN |
| Parental | KQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMT |
| KQQ.DIAVNWAGGLHHAKK..ASGFCY..D...A.LELLKYHQRVLY.D.DIHH.DG.EE.FY.T..V.T | |
| Retrocopy | KQQMDIAVNWAGGLHHAKKFKASGFCYISDTIWATLELLKYHQRVLYVDVDIHHDDGMEETFYITGQVRT |
| Parental | VSFHKYGEYFPGTGDLRDIGAGK-GKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSD |
| VSFHKYGEYFPG.GDL.DIG.GK.G.YYAVN..L.DGID.ES.EAI.K.VMSKV.EM...S..VL...SD | |
| Retrocopy | VSFHKYGEYFPGNGDLWDIGTGK<GRYYAVNCLLLDGIDYESCEAILKLVMSKVIEMLLSSVMVLWHVSD |
| Parental | SLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYF |
| .L..D.L.CFNLT.K.HAKC.EFVKSFNLP.L....GGYTI.NVA.CW..E.AVALD.E..NE..YND.F | |
| Retrocopy | ALFRDQLDCFNLTMKAHAKCMEFVKSFNLPILLMAEGGYTIYNVAQCWK*EIAVALDMETSNEPSYND*F |
| Parental | EYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKR |
| EYF.P.FK..ISPSNMTN.NTNEYLEKIK..LFENL.M.PH...VQMQ.IPEDA.P.E.G....E..... | |
| Retrocopy | EYFRPYFKPYISPSNMTN*NTNEYLEKIK*WLFENLVMQPHPSAVQMQVIPEDAVPQE-GGIENEEDPDK |
| Parental | -ISICSSDKRIACEEEFSDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAK |
| .ISIC.SD.RI.CEEEF..S.EEGEGGRK.S..F.K.KRVKT....E.....KK......KTKE.KP.AK | |
| Retrocopy | >ISICFSDRRITCEEEFFGSDEEGEGGRKISPIFRKSKRVKTG*KRETQR*RKKS-QKRRKTKEKKPGAK |
| Parental | GVKEEVKLA |
| .VK..VKLA | |
| Retrocopy | EVKDQVKLA |
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 | 7 .62 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 7 .54 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 5 .10 RPM |
| SRP007412_heart | 0 .00 RPM | 12 .37 RPM |
| SRP007412_kidney | 0 .00 RPM | 34 .86 RPM |
| SRP007412_liver | 0 .00 RPM | 24 .34 RPM |
| SRP007412_testis | 0 .15 RPM | 83 .64 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1085 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1085 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_1085 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_826 |
| Gorilla gorilla | retro_ggor_676 |
Parental genes homology:
Parental genes homology involve 15 parental genes, and 21 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ciona intestinalis | ENSCING00000002649 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000000970 | 2 retrocopies | |
| Homo sapiens | ENSG00000116478 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000011741 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000013837 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000009948 | 2 retrocopies |
retro_mmul_1085 , retro_mmul_2518,
|
| Macaca mulatta | ENSMMUG00000012588 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000028800 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000002473 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000005709 | 3 retrocopies | |
| Pelodiscus sinensis | ENSPSIG00000004134 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000013325 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000009568 | 3 retrocopies | |
| Sarcophilus harrisii | ENSSHAG00000008787 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000001613 | 1 retrocopy |