RetrogeneDB ID: | retro_mmul_2227 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 7:55241284..55242912(-) | ||
| Located in intron of: | ENSMMUG00000011045 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TYRO3 | ||
| Ensembl ID: | ENSMMUG00000013803 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mmul_2227
ATGGCGCTGAGGCGGAGCATGGGGCGGCCAGGTCTCCCGCTGCTGCGGCCGCCGCTGGGGCTGCCATTGGCAGCTCTGGC
TTCTCTGCTGCTGCAGGTCTGGGGCTGCAGGTCCGAAGCTCAACAGAGCCCTGGTGAAGCTGACAGTGGCTCAGGGGCAG
CTGGTGAAGCTCAACTGCAGCATGGAGGGGATGGAGGAGCCTGACATCCAGCTGGTGAAGGATGGGCCTGTGATCCAGAA
CTTGGACCAGTTGTACACCCCAGTCAGCAAGCAGCACTGGATCGACTTCCTCAGCCTGAAGTCAGTGGAGCGCTCTGACG
CGGCCAGTACTGGTGCCAGGTGGAGAATGGGGGCAAAACCAAGATCTCCCAGCCAATGTGGCTCATGGTAGAAGGTGTGC
CACTTTTCGCAGTGGAGCCAAAAGATCTGGCAGTGCCACCCAATGCCCCTTTCCAACTGTCTTGCAAGGCTGTGGGTCCC
CCTGAAGCTGTTACCATTGTCTGGTGGAGAGAAACTATCAAGACCGGGAGACCCGCTCCCTCTCCATCTGTTTTAAATGT
AACAGGGGTGACCCAGAGCACCCATGTTTTCCTGTGAAGCTCACAACCTAAAATGCCTGGCCTCTTCTCGCATAGCCACT
GTTCACCTTCAAGCACTGCCTGCAGCCCCCTTCATCATCACCGTGACAAAGCTTTCCAGCAGCAACATTAGTGTGGCCTG
GATGCCAAGTGCTGATGGCTGAGCCCTGCTATAGTCCCGTACAGTTCAGGTAACACAGGCCCCAGGAGGCTGGGAAAGTC
CTGGCTGTTGTGGTCCCTGTGGCCCCCTTTACCTGCCTGCTCCGGGAGCTGGTGCCTGCCATCAGCTACAGCCTCAGGGT
GCACTGTGCCAATGCCTTGGGGCCCTCTCCCTATGCTGACTGGGTGCCCTTTCAGACCAAGGGTCTGGCCGCAGCCAGCA
CTCCCCAAAATCCCCATGCCATCTGCACAGATTCAGGCCTCATCTTGGAGTGGGAAGAAGTGATCCCCAAGGGCCCTTTG
GAAGGCCCCCTGGGACCCTGTAAACTGTCCTGGGTTCAAGACAGTGGAACCCAGGATGAGCTGACAGTGGAAGGGAGCAG
GACCAATTTGACAGGCTGGGATACCCAAAAGAACCTGATCATACGTGTGTGCGTCTCCAGTGCAGTTGGCTGTGGACCGT
GGAGTCAGCCACTGGTGGTCTCTTCTCATGACCATGCAGGCCAGCAGGGCCGTCCTCACAGCCGCACATCCTGGGTACCT
GTGGTCCTTGGTGTGCTAACGGCCCTGGTGATGGCTGCTGCCCTGGCCCTCATCCTGCTTCGAAAGAGACGGAAAGAGAC
ACGGTTTGGGCAAGGCTTTGACTGTGTCATGGCCCGGGGAGAGCCATCTGTTTACTTCCGGGCAGCCCAGTCCTTCAATC
GAGAAAGGCCCGAGTGCATCGAGGCCGCATTGGACAGCTTGAGCATCAACAGTGGACTAAAGGAAAAACAAGGATGTGCT
CAGCCCAGAGCAGCAGTTCACCCTGGCCAGATGTTGGGCAAAGGAGAGTGTGGTTCAGTGCGGTAGGCCCAGCTGAAGCA
GGAGGATGGCTCCTTTGTGAAAGATGCT
ORF - retro_mmul_2227 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.9 % |
| Parental protein coverage: | 61.98 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MALRRSMGRPGLPPLLLPPPPRLGLLLAALASLLLPE-SAAAGLKLMGAPVKLTVSQGQPVKLNCSVEGM |
| MALRRSMGRPGLP..LL.PP..LGL.L.A....LL...S.AAG.KL..A.VKLTV.QGQ.VKLNCS.EGM | |
| Retrocopy | MALRRSMGRPGLP--LLRPP--LGLPL-AALASLLLQ>SGAAGPKLNRALVKLTVAQGQLVKLNCSMEGM |
| Parental | EEPDIQWVKDGAVVQNLDQLYIPVSEQHWIGFLTARLLKSAERSDA-GRYWCQVEDGGETEISQPVWLTV |
| EEPDIQ.VKDG.V.QNLDQLY.PVS.QHWI.FL....LKS.ERSDA.G.YWCQVE.GG.T.ISQP.WL.V | |
| Retrocopy | EEPDIQLVKDGPVIQNLDQLYTPVSKQHWIDFLS---LKSVERSDA<GQYWCQVENGGKTKISQPMWLMV |
| Parental | EGVPFFTVEPKDLAVPPNAPFQLSCEAVGPPEPVTIVWWRGTTKIGGPAPSPSVLNVTGVTQST-MFSCE |
| EGVP.F.VEPKDLAVPPNAPFQLSC.AVGPPE.VTIVWWR.T.K.G.PAPSPSVLNVTGVTQST.MFSCE | |
| Retrocopy | EGVPLFAVEPKDLAVPPNAPFQLSCKAVGPPEAVTIVWWRETIKTGRPAPSPSVLNVTGVTQST>MFSCE |
| Parental | AHNLKGLASSRTATVHLQALPAAPFNVTVTKLSSSNASVAWMPGADGRALLQSCTVQVTQAPGGWE-VLA |
| AHNLK.LASSR.ATVHLQALPAAPF..TVTKLSSSN.SVAWMP.ADG.ALL.S.TVQVTQAPGGWE.VLA | |
| Retrocopy | AHNLKCLASSRIATVHLQALPAAPFIITVTKLSSSNISVAWMPSADG*ALL*SRTVQVTQAPGGWE>VLA |
| Parental | VVVPVPPFTCLLRDLVPATNYSLRVRCANALGPSPYADWVPFQTKGLAPASAPQNLHAIRTDSGLILEWE |
| VVVPV.PFTCLLR.LVPA..YSLRV.CANALGPSPYADWVPFQTKGLA.AS.PQN.HAI.TDSGLILEWE | |
| Retrocopy | VVVPVAPFTCLLRELVPAISYSLRVHCANALGPSPYADWVPFQTKGLAAASTPQNPHAICTDSGLILEWE |
| Parental | EVIPEGPLEGPLGPYKLSWVQDNGTQDELTVEGTRANLTGWDPQKDLIVRVCVSNAVGCGPWSQPLVVSS |
| EVIP.GPLEGPLGP.KLSWVQD.GTQDELTVEG.R.NLTGWD.QK.LI.RVCVS.AVGCGPWSQPLVVSS | |
| Retrocopy | EVIPKGPLEGPLGPCKLSWVQDSGTQDELTVEGSRTNLTGWDTQKNLIIRVCVSSAVGCGPWSQPLVVSS |
| Parental | HDHAGQQGPPHSRTSWVPVVLGVLTALVTAAALALILLRKRRKETRFGQAFDSVMARGEPAVHFRAARSF |
| HDHAGQQG.PHSRTSWVPVVLGVLTALV.AAALALILLRKRRKETRFGQ.FD.VMARGEP.V.FRAA.SF | |
| Retrocopy | HDHAGQQGRPHSRTSWVPVVLGVLTALVMAAALALILLRKRRKETRFGQGFDCVMARGEPSVYFRAAQSF |
| Parental | NRERPERIEATLDSLGISDELKEKLEDVLIPEQQFTLGRMLGKGEFGSVREAQLKQEDGSFVKVA |
| NRERPE.IEA.LDSL.I...LKEK......P......G.MLGKGE.GSVR.AQLKQEDGSFVK.A | |
| Retrocopy | NRERPECIEAALDSLSINSGLKEK-QGCAQPRAAVHPGQMLGKGECGSVR*AQLKQEDGSFVKDA |
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 .11 RPM | 51 .99 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .56 RPM | 159 .77 RPM |
| SRP007412_cerebellum | 0 .06 RPM | 36 .29 RPM |
| SRP007412_heart | 0 .18 RPM | 1 .35 RPM |
| SRP007412_kidney | 0 .12 RPM | 6 .81 RPM |
| SRP007412_liver | 0 .16 RPM | 0 .67 RPM |
| SRP007412_testis | 0 .00 RPM | 13 .76 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2227 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2227 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_2227 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000092445 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000013803 | 1 retrocopy |
retro_mmul_2227 ,
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