RetrogeneDB ID: | retro_mmul_2040 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 6:127427179..127428574(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SUGP1 | ||
| Ensembl ID: | ENSMMUG00000028834 | ||
| Aliases: | SUGP1, SF4 | ||
| Description: | SURP and G patch domain containing 1 [Source:HGNC Symbol;Acc:18643] |
Retrocopy-Parental alignment summary:
>retro_mmul_2040
ATCAAAGTTTCACCCCCAGAGGGAGTTGAGACTCAGAAAGTGATAGAGAAACTGGCCAATTTGTGGCAGAAGCAGGCCCC
GAGTTAGAAAAAGCGACTATGGAGGACTACAGGGATAACCCGGCGTTTCCATTTTTGCACGGTAAGAATAGCAGGCAATT
CCTCTACTACAGAAAGGAGGTGGCTGAGATAAGAAAGGAAGCGCGGAAGTTGCAGGCAGCCTCTCAGAAAGTTTCACCCC
CAGAGGACGAAGAGGTCAAGAACCTTGCAGAAAAGTTGGCCAGGTTCATAACGGGCGGGGATCCCGAGGTGGAAACCATC
GCCCTCCAGAACAACCGCGAAAACCCAGGCGTTCAGCTTTCTGTACGAGCCCAACAGCCAAGGGTCCAACTGCTACTAAC
AGAAGCTGGAGGAGTTCCGGAAAGCCAAGGCCGGCTCCACAGGCACCCTCACGGCACCCGACCCCGGCCTGAAGCGCAGG
TCCCCTCCTGAGGCCCTGTCAGGGCCTTCGCCCCCGACAATCACCTGCCCCGCCTCGTCCTCGCCTGTGCCCCCCCATCA
TCCCTGCTCCAGGCGCCCCCGGGAAGCCAGCCTCCGCAGCCACCGTCAAAAGGAAGCCGAAGAGCCGAAGAGCCGGCGGA
GGCCTGAAGAGAACAAAGTAGAGCTCTCACCTGCTGAGCTGGTGCAGAGGGACGTGGCTGACTCTCCCTCACCTCTGTCA
GTTCAGGACCTCAAGGGGCTCAGCTATGAGAACTGGAAGTCCGTGGGTCTAGTGGGTCTCACGGAGCTATCGGGCTCCCA
GAAGCAGCAGCTGAAGGACCATCAGGAGATGCATCAGATGTACGACATGATCCTGCAGCAAAAGCGGGCCTTGCAGGACA
TGCAGCTGCTGTGGGAGAAGGCGGTGCAGCAGCACCAGCACGGCTACCACAGCGACGAAGAGGTGAACAGCGAGTTGGTC
ACCTGGGAGCACCAGCTGCAGCGCATGGAGATGAACAACATGAGGTAATGGGCCGACCAGCTGACGAAGATGGGCCTGGG
CAAGCACTTCATCCCAGACTTCCTGCCTCCAGACAAGCTGGAGAAGTTTAGGGAGACCTTCAAGGAGGGCCGCGAGCCTG
ACTACTCGGAGTACGAGGAGTTCAAACTGACGGAGGAGAATATCGGCTACCAGATGCTGATGAAGATGGGCTGGAAGGAG
GGCGAGGGGCTGGGCTCGGAGAGCCAGGGCATCAAGAATCCGGTCAACAAGGGCACCACCGCAGTGGCTGGCGCCGGCTT
CCGCATTGACCAGCCGGCCGCTCTCTCCAAGGAGTACAACGAGTACTAGGCCTTCCGCAAGAGGATGATGCCCGCCTACC
GCTTCCGGCCCAACCCCCCGGAACAACCTCAGAGG
ORF - retro_mmul_2040 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.39 % |
| Parental protein coverage: | 81.87 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LKVSPPEGAETRKVIEKLA-RFVAEGGPELEKVAMEDYKDNPAFAFLHDKNSREFLYYRKKVAEIRKEAQ |
| .KVSPPEG.ET.KVIEKLA..FVAE.GPELEK..MEDY.DNPAF.FLH.KNSR.FLYYRK.VAEIRKEA. | |
| Retrocopy | IKVSPPEGVETQKVIEKLA<QFVAEAGPELEKATMEDYRDNPAFPFLHGKNSRQFLYYRKEVAEIRKEAR |
| Parental | KSQAASQKVSPPEDEEVKNLAEKLARFIADGGPEVETIALQNNREN-QAFSFLYEPNSQGYKYYRQKLEE |
| K.QAASQKVSPPEDEEVKNLAEKLARFI..G.PEVETIALQNNREN.QAFSFLYEPNSQG...Y.QKLEE | |
| Retrocopy | KLQAASQKVSPPEDEEVKNLAEKLARFITGGDPEVETIALQNNREN>QAFSFLYEPNSQGSNCY*QKLEE |
| Parental | FRKAKASSTGSLTAPDPGLKRKSPPEALSGSLPPATTCPASSTPVPT-VIPAPAA---PGKPASAATVKR |
| FRKAKA.STG.LTAPDPGLKR.SPPEALSG..PP..TCPASS.PVP...IPAP.A...P...A....... | |
| Retrocopy | FRKAKAGSTGTLTAPDPGLKRRSPPEALSGPSPPTITCPASSSPVPP>IIPAPGAPGKPASAATVKRKPK |
| Parental | KR-KSRWGPEEDKVELPPAELVQRDVDASPSPLSVQDLKGLGYEKGKPVGLVGVTELSDAQKKQLKEQQE |
| .R.KSR..PEE.KVEL.PAELVQRDV..SPSPLSVQDLKGL.YE..K.VGLVG.TELS..QK.QLK..QE | |
| Retrocopy | SR<KSRRRPEENKVELSPAELVQRDVADSPSPLSVQDLKGLSYENWKSVGLVGLTELSGSQKQQLKDHQE |
| Parental | MQQMYDMIMQHKRAMQDMQLLWEKAVQQHQHGYDSDEEVDSELGTWEHQLRRMEMDKTREWAEQLTKMGR |
| M.QMYDMI.Q.KRA.QDMQLLWEKAVQQHQHGY.SDEEV.SEL.TWEHQL.RMEM...R.WA.QLTKMG. | |
| Retrocopy | MHQMYDMILQQKRALQDMQLLWEKAVQQHQHGYHSDEEVNSELVTWEHQLQRMEMNNMR*WADQLTKMGL |
| Parental | GKHFIGDFLPPDELEKFMETFKALKEGREPDYSEYKEFKLTVENIGYQMLMKMGWKEGEGLGSEGQGIKN |
| GKHFI.DFLPPD.LEKF.ETFK...EGREPDYSEY.EFKLT.ENIGYQMLMKMGWKEGEGLGSE.QGIKN | |
| Retrocopy | GKHFIPDFLPPDKLEKFRETFK---EGREPDYSEYEEFKLTEENIGYQMLMKMGWKEGEGLGSESQGIKN |
| Parental | PVNKGTTTVDGAGFGIDRPAELSKEDDEYEAFRKRMMLAYRFRPNPLNNPRR |
| PVNKGTT.V.GAGF.ID.PA.LSKE..EY.AFRKRMM.AYRFRPNP...P.R | |
| Retrocopy | PVNKGTTAVAGAGFRIDQPAALSKEYNEY*AFRKRMMPAYRFRPNPPEQPQR |
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 | 25 .88 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 43 .23 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 27 .12 RPM |
| SRP007412_heart | 0 .00 RPM | 22 .08 RPM |
| SRP007412_kidney | 0 .00 RPM | 20 .54 RPM |
| SRP007412_liver | 0 .00 RPM | 28 .18 RPM |
| SRP007412_testis | 2 .90 RPM | 111 .76 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2040 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2040 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_2040 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005755 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000028834 | 1 retrocopy |
retro_mmul_2040 ,
|
| Tarsius syrichta | ENSTSYG00000005329 | 1 retrocopy |