RetrogeneDB ID: | retro_mmul_1709 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 3:108183772..108184725(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MMU.13619 | ||
| Ensembl ID: | ENSMMUG00000011423 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mmul_1709
AGAACCTGCAGTGTAATGACAACAGTTAAGTCCAGGCCATTTTGGGAAAAGCAAGGGAAGATACTGCTGAAAGGTCGCAG
GCTCCTTATAGACGCTCTCAAGGCTGGAGCTGTGCCAACAGTTTTCTTCTCTAGCCATCTATAATACATAAAGAAGCTGC
TCATCGATAAGCCGAAGGGTGTCAGCCTCATTAAGATGAAATTCGAGGACATGAGGGATTGGTCCAACCTAGTAATGCCA
CAAAAATAATGGGGATTTTTGCCAAACCTGACCATGTTAACATGACATATCCAAAGACTCAGCTTTAGCACTCACTGCCT
TTGTTATTGATTTGTGACAATCTCTGTGACCCTGGGAATCTGGGGACAATTCTGAGATCTCCAGCTGGGGCGGGCTGCAG
CAAAGTGTTAGTCATTTTGAAATGTGTGGATGCCTAGGAGCCCAAAGTGCTACGGGTGGTTATGGGTGTACTTTTCCCGG
TGCCCATTATCAGTAGTCTGAAAACAAAAACAGTGGCAAATTACCTGCCCCCTGACACCCAGGTCTGTTTGGCTGACAAC
CGAAGCCTTTATGCTGAGGCTCAGATGTCTAATAAAGACAGTGACTATGGCTGGGTGTGTGATTGGCGATTCCTGAAGTT
TCACAAGTACGAAGAAAAGGAAGGTCTAGAAACTGGAGCCAGTAAAGGTTTGCTACCTGTTATTGAGGTTCAGAGTTATG
GCTTCGACTGGACAGAGGCACCAGCAGCTGCAGTGGTTGGCAGCGAGACCTACGGCATGAACCTGGATTCTCTGTAGTTG
GCCGAGAGCCCTGGGGGCAACAGGCTGCTGATCCCTGTTGCACCTGGTGTGGACAGCCTCAACTCAGCCATGGCTGCACG
CATCCCGCTTTTTGAAGGGAAAAGACAACTGTGGGTGAGGGCGGAACACTTGAGCAGGGACAGGAGTTACCAC
ORF - retro_mmul_1709 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.04 % |
| Parental protein coverage: | 75.71 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RLSSVMTIVKSRPFREKQGKILLEGRRLITDALKAGAVPKMFFFSRLEYLKELPVDKLKGVSLIKVKFED |
| R..SVMT.VKSRPF.EKQGKILL.GRRL..DALKAGAVP..FF.S.L.Y.K.L..DK.KGVSLIK.KFED | |
| Retrocopy | RTCSVMTTVKSRPFWEKQGKILLKGRRLLIDALKAGAVPTVFFSSHL*YIKKLLIDKPKGVSLIKMKFED |
| Parental | IKDWSNLVTPQG-IMGIFAKPDHVKMAYPKTQLQHSLPLSLICDNLRDPGNLGTILRSAAGAGCSKVLLT |
| ..DWSNLV.PQ..IMGIFAKPDHV.M.YPKTQL.HSLPL.LICDNL.DPGNLGTILRS.AGAGCSKVL.. | |
| Retrocopy | MRDWSNLVMPQK<IMGIFAKPDHVNMTYPKTQL*HSLPLLLICDNLCDPGNLGTILRSPAGAGCSKVLVI |
| Parental | KGCVDPWEPKVLRAGMGAHFQVPIINNLEWETVPNYLPPDTRVYVADNCGLYAQAQMSNKASDHGWVSNQ |
| ..CVD..EPKVLR..MG..F.VPII..L...TV.NYLPPDT.V..ADN..LYA.AQMSNK.SD.GWV... | |
| Retrocopy | LKCVDA*EPKVLRVVMGVLFPVPIISSLKTKTVANYLPPDTQVCLADNRSLYAEAQMSNKDSDYGWVCDW |
| Parental | RLLKFQKYEEEEDVETGASQDWLPDVEVQSYDSDWTEAPAAVVIGGETDGVSVESLQLAESTGGKRLLIP |
| R.LKF.KYEE.E..ETGAS...LP..EVQSY..DWTEAPAA.V.G.ET.G....SL.LAES.GG.RLLIP | |
| Retrocopy | RFLKFHKYEEKEGLETGASKGLLPVIEVQSYGFDWTEAPAAAVVGSETYGMNLDSL*LAESPGGNRLLIP |
| Parental | VVPGVDSLNSAMAASILLFEGKRQLRGRAEHLSRDRSHH |
| V.PGVDSLNSAMAA.I.LFEGKRQL..RAEHLSRDRS.H | |
| Retrocopy | VAPGVDSLNSAMAARIPLFEGKRQLWVRAEHLSRDRSYH |
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 | 5 .15 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 18 .25 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 6 .52 RPM |
| SRP007412_heart | 0 .00 RPM | 5 .71 RPM |
| SRP007412_kidney | 0 .00 RPM | 6 .57 RPM |
| SRP007412_liver | 0 .00 RPM | 8 .95 RPM |
| SRP007412_testis | 0 .08 RPM | 11 .16 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1709 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1709 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_1709 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3704 |
| Gorilla gorilla | retro_ggor_2505 |
| Pongo abelii | retro_pabe_3149 |
| Callithrix jacchus | retro_cjac_3130 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000021701 | 1 retrocopy | |
| Homo sapiens | ENSG00000171861 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000015518 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000011423 | 1 retrocopy |
retro_mmul_1709 ,
|
| Nomascus leucogenys | ENSNLEG00000000570 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000007762 | 1 retrocopy |