RetrogeneDB ID: | retro_mdom_849 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 2:190805987..190807710(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LRP10 | ||
| Ensembl ID: | ENSMODG00000005233 | ||
| Aliases: | None | ||
| Description: | low density lipoprotein receptor-related protein 10 [Source:HGNC Symbol;Acc:14553] |
Retrocopy-Parental alignment summary:
>retro_mdom_849
TTTCTGCTTTCCTATATGCTAGTCGATTCATATGCCTCCTAGAAGAGTTCTGATGCCTGAACCGCAGATGTGTGCCAAAG
ATCCAGTGCTGTGATGGGATGGATAACTGTGGTGACCAATCTGATGAGACTGACTGTAGCCCAAGCCTTTTCCATAGCTT
GACTGCTGTCCCTGCCCCTGCCTGCAACCGTACCTTGGAAGACTTCTACCGGGTCTTTTCTTCCCGGAGCTATTCCCTCT
CTGCCCTATACCCAACCCCTCACTCCTGCCTCTGGCTGCTGGATCCCCATGATGGGCGAAGGCTCATCGTGCATTTTACC
ACCCTAGAGCTAAGCAAATGGGATTCAGAGCATGTGTATGACGGTCCTGGACCTCCAGATCCTTCTCACCTGCTCCGAAG
CCTTAACTATTTCAGCAATGGCAAAGCAATCATGGTGGAGACGCTCTCAGGCAAGGCTACTGTGACCTACCACATGGGGC
CGTGGAGCAAGGGTGGGTTCAATACCACCTACCATGTGAAAGGATACTGTCTGCCCTGGGACCGACCCTGTGGTGCTGGC
TCTGGAGAGGGTCCTGGGGAGGGTCCAGGAGAGGGCTGCTATAGTGAAGCCCAGCGGTGTGATGCGATCTGGGACTGTGC
CGATGGCACAGATGAAAAAGACTGCCCGGGATGCCTGTCTGGGCGCTATTCCTGTGGGGCTCCGGGAACCCCTGGTGCCA
CAGCCTGCTACCCCTCTGCCGATCGCTGCGACTACCAGACCTTTTGCGTGAACCGGGCAGATGAACAGCAGTGCCATCAC
TGCCAGCCAGGCAACTTCCGGTGCAGGGATGCTCGGTGTGTGTATGCAACTTGGGTATGTGATGGGCAGCCCGACTGCTC
TGATGGCAGCGACGAATGGGACTGTGCCTGTGCCCTGCCCCGAAAAGTCATCATGGCTGCCGCCATCGGCAGCTTGATCT
GCGGCCTGCTGCTTGTCATCGCCCTGGGATGTACCTGCAAACTCTATGCCCTCCACACGCAAGAATACAGCATCTTTGCC
CCCCTTTCAAGAGTGGAGGCCGAGATTGTACAGCAGCAAGCACCTCCATCCTATGGCCAGCTTATTGCTCACGGTGCCAT
CCCGCCTGTAGATGACTTTCCAACTGAGAACCCCAACGATAATTCAGGCCTGGGGAACCTTTGATCTCTGCTACAAATCC
TGCGCCAGGATGTGTCTTCAGGGAGTTCATCGAGTGCCTGCCGTTGCCAAGGCAGGTCTGCACAACGACTGGTCTGCCGC
CTCCGTCAGTGGGGCTTGCTTCCTGTGCATTCCCCCTGCAGGTCCCCTGACTCAGCTCAGACTGCATCTGCCCCATCTAC
TGTTGACGCCCCAGAGGGCAGTCAGGATACTCCTTTAGAAGGAGCAATGGGTGGATGAGATCCAGAGGAGGCCCCTCCAC
TGCCCATGAAGGTGCCCCTTTCTTCTACCAACTCCCCCTGCATACCCCCTGAGGACCCACCCCTCCAATCACTCCCCCTC
CACTCCCATCATCCCTGTTGTCTGGGATGGTACAGGCCCTTTGTGGCCGCCTCATGCCCAGTCTTCGGTCCCCTACTCCC
CCCCAAGCTATGCCAGACCCTCGAACAGTGCCCCCATCCCAAGAAGATGAGGATGATGTGCTGCTACTCCCTCTGGCAGA
ACCCAGGCCCTGGGTAGGGGAGGAGGATGAGCCACTGCTGACC
ORF - retro_mdom_849 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.59 % |
| Parental protein coverage: | 81.41 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | FLLSYML-DRFICLREEFRCLNRRCVPRIQRCDGIDNCGDQSDETDCSPSLFHSLTAVPTPACNRTLEDF |
| FLLSYML..RFICL.EEF.CLNRRCVP.IQ.CDG.DNCGDQSDETDCSPSLFHSLTAVP.PACNRTLEDF | |
| Retrocopy | FLLSYML<SRFICLLEEF*CLNRRCVPKIQCCDGMDNCGDQSDETDCSPSLFHSLTAVPAPACNRTLEDF |
| Parental | YGVFSSPSYSLSALYPSPHSCLWLLDPHDGRRLIVRFTTLELGKWDSVHVYDGPGPPDPSRLLRSLNYFS |
| Y.VFSS.SYSLSALYP.PHSCLWLLDPHDGRRLIV.FTTLEL.KWDS.HVYDGPGPPDPS.LLRSLNYFS | |
| Retrocopy | YRVFSSRSYSLSALYPTPHSCLWLLDPHDGRRLIVHFTTLELSKWDSEHVYDGPGPPDPSHLLRSLNYFS |
| Parental | NGKAIMVETLSGKATVTYHMGPWSKGGFNATYHVKGYCLPWDRPCGAGSGEGPGEGPGEGCYSEAQRCDG |
| NGKAIMVETLSGKATVTYHMGPWSKGGFN.TYHVKGYCLPWDRPCGAG............CYSEAQRCD. | |
| Retrocopy | NGKAIMVETLSGKATVTYHMGPWSKGGFNTTYHVKGYCLPWDRPCGAGXXXXXXXXXXXXCYSEAQRCDA |
| Parental | IWDCADGTDEKDCPGCLPGRYPCGAPGTPGATACYPSADRCNYQTFCVNGADEQQCRHCQPGNFRCRDDR |
| IWDCADGTDEKDCPGCL.GRY.CGAPGTPGATACYPSADRC.YQTFCVN.ADEQQC.HCQPGNFRCRD.R | |
| Retrocopy | IWDCADGTDEKDCPGCLSGRYSCGAPGTPGATACYPSADRCDYQTFCVNRADEQQCHHCQPGNFRCRDAR |
| Parental | CVYETWVCDGQPDCSDGSDEWDCAYALPRKVITAAVIGSLICGLLLVIALGCTCKLYAIRTQEYSIFAPL |
| CVY.TWVCDGQPDCSDGSDEWDCA.ALPRKVI.AA.IGSLICGLLLVIALGCTCKLYA..TQEYSIFAPL | |
| Retrocopy | CVYATWVCDGQPDCSDGSDEWDCACALPRKVIMAAAIGSLICGLLLVIALGCTCKLYALHTQEYSIFAPL |
| Parental | SRVEAEIVQQQAPPSYGQLIAQGAIPPVDDFPTENPNDNSVLGNLRSLLQILRQDVSSGGSSSARRRQRG |
| SRVEAEIVQQQAPPSYGQLIA.GAIPPVDDFPTENPNDNS.LGNL.SLLQILRQDVSSG.SSSA.R.Q.G | |
| Retrocopy | SRVEAEIVQQQAPPSYGQLIAHGAIPPVDDFPTENPNDNSGLGNL*SLLQILRQDVSSGSSSSACRCQ-G |
| Parental | RSARRLVRRLRRWGLLPRANPPSRAPDSSLQTASTPSTTDTPEGSQGTPLEGAMGGRDPEEAPPLPVKVP |
| RSA.RLV.RLR.WGLLP....P.R.PDS..QTAS.PST.D.PEGSQ.TPLEGAMGG.DPEEAPPLP.KVP | |
| Retrocopy | RSAQRLVCRLRQWGLLP-VHSPCRSPDSA-QTASAPSTVDAPEGSQDTPLEGAMGG*DPEEAPPLPMKVP |
| Parental | LSSTNSPCIPPEDPP-PPITPPPPPSSLLSGVVQALRGRLMPSLRSPTPPQAIPDPRTVPPSQEEEDDVL |
| LSSTNSPCIPPEDPP.PPITPPP.PSSLLSG.VQAL.GRLMPSLRSPTPPQA.PDPRTVPPSQE.EDDVL | |
| Retrocopy | LSSTNSPCIPPEDPP<PPITPPPLPSSLLSGMVQALCGRLMPSLRSPTPPQAMPDPRTVPPSQEDEDDVL |
| Parental | LLPLAEPGPWVGEEDEPLLT |
| LLPLAEP.PWVGEEDEPLLT | |
| Retrocopy | LLPLAEPRPWVGEEDEPLLT |
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 | 161 .15 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 183 .79 RPM |
| SRP007412_heart | 0 .00 RPM | 444 .75 RPM |
| SRP007412_kidney | 0 .00 RPM | 1062 .68 RPM |
| SRP007412_liver | 0 .00 RPM | 509 .03 RPM |
| SRP007412_testis | 0 .00 RPM | 165 .20 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_849 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_849 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000005233 | 1 retrocopy |
retro_mdom_849 ,
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