RetrogeneDB ID: | retro_rnor_372 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 7:15526033..15528817(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000026582 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Phf8 | ||
| Ensembl ID: | ENSRNOG00000002708 | ||
| Aliases: | Phf8, RGD1561065 | ||
| Description: | histone lysine demethylase PHF8 [Source:RefSeq peptide;Acc:NP_001101723] |
Retrocopy-Parental alignment summary:
>retro_rnor_372
ATGGCCTTGGTGCCTGTGTATTGTCTTTGTAGACAGCCTTACAATGTGAACCACTTCATGATTGAGTGTGACCTGTGCCA
GGACTGGTTTCATGGTAGTTGTGTTGGGATTGAAGAAGAAAAAGCTGTTGACATCGACATCTACCACTGCCCAGACTGTG
AGGTCATATATGGACCCTCCATTATGAAAAAATGGCCTGCATCGTCTAAAGAGCACGAAGCTCTCAAGAGGGAGCCAGTG
AAGACTGGGAGCCCTATCTTTATTCACCAGCTCCAGGGTAAGACTTTTGACAGCTCTGACGAAGTGATCTTGAAGCCCAC
AGGAAGTCAGTTGACAGTGGAATTCTTGGAAGAAAGTAGCTTCAGTATACCTATCCTTGTCTTGAAGAAGAATGGGTTGG
GGATGACCCTTCCCCCAACATCATTCACTGTCAGAGATGTGGAACAATATGTTGGTTCTGACAGAGAGATTGACGTGATT
GATGTGGCCTGTCAGGCTAGCAGCAAGATGATGCTGGGTGATTTTGTGAAATATTATTACAGCAGAAGGAGGGAAAAAGT
ATTTAATGTTATTAATCTGGAATTCTCTAATACTAGGCTTTCTAATACAGTAGAGATGCCCAAGATAGTTCGTAAGCTTT
CCTGGGTTGAAAACTTATGGCCAGAAGAGTGTGGCTTTGAGAGACCCACTGTACAGAAGTATTGCCTTATGAGTGTGCAG
AATAGCTATACTGATTTTCACATTGAATTTGGTGGCACTTCGATCTGGTACCATGTACTTAAGGGTGAGAAGATCTTCTA
CCTGATCCACCCAACAGATGCTAACCTGACTCTTTTTAAATGTTGGAGCAACTCTTCTAACCAAAAAGAAATGTTCTTTG
GTGACCAGGTAGACAAATGTTACAAGTGTTCTGTGAAGCAAGGACAGACACTTTTCATTCCCACAGGATGGATCTATGCT
GTGCTGACCCCTGTCGACTGCCTGGCATTTGGAGGAAACTTCTTACACAGCCTCAACATTGAAATGCAGCTCAAAGCCTA
CGAGACTGAGAAACATCTGAGTACAGCACACCTCTTCAAGTTTCCAAGCTTTGAGACCATCTGTTGGCATGTGGGAAAGC
ACATGCTGGACATCTTTGAAGGTTTGCGGGAGAATGGGAGATACCCTGCACCCTACTTGGTTCGTGGTGGTAAAGCTCTA
AATTTGGCCTTCCAAGCTTGGACAAGGAAAGAAGTTCTGCCAGACCATGAGGATGAGATCCCAAAGACAGTGCAGACCGT
ACAGCTCATTGAAGATCTGGCTAGGGAAATCTGTCTGGTCGAAGATACCTCCCAACAGAGCATCCCAAAGACAAGTACCA
TCTTTGGGCTCCAGCAACACCATACCAATCCCTCTTCCTTAAATAGGCAAACTCATTCCACTTCAGTATCCACGTCTACA
TTATCACTGCCCTCCAAAAGTGGTTCGGAAAAGAAAAGCCCGAAGTATAAAGACATCTTCAAGAAGGAAGAACAAACAAG
CAAGGAGAGACCAACTTTGGGGCCTAATGACCAACATAGCTGTAATTTCATGGATCTAAATAATCATCAAGAACTGAAGG
TAGGCTTTTCCCAAAATGTAGAGTGTAACATCACTAGTACGTGTTTGAATGACTCAGATGATGACTCAAAATTTGACAAA
GTCTGTGATGGGAATGAGAGCCTGGTCCCTCTGTTGATGGCTAATGGCAGTACCAAGAGGGTGAAGAGCTTGTCCAATTC
TTGGCGAGCCAAAATCACAAAGAAGGAAGATAAATCAAAGTTGGTAGAAGAAAAAAAGATGGGAGACAAGTTTGACTTGG
ATACAAATGATGAGCTGCAGACTGAAAAAAGATTGGGCAAAGTAAAAGATAGTCTAGTAGTAAGGTCAAAAATTCCCCCA
AATTTGCCCCATGTGAAGTTTTGCTCTCACCAAAACCAAAGTTGTGAACCAGGGGAAACTGAAATTGACATTGTGGAGAA
CTATAAAATAGATGAGGGAATGATGGAAGGGGTTGAAGGCAAACTTAAGAATGGAGGTGAATCTGATGGAATTCTTGATC
TACTTAAGGCCAGGAAACAGGTGGGAGGACCTGGCTATGTTGTCCTCACTGATGCCCCAGACTATTCCAGCAGTAAGGAG
AATACCCAGGACACTGTGTTCATGGCTGAATTGCAGTCCTCCTCTCCTTCACCAGCTCCTTCCACCCTTCATACACTTTG
GAGTGGGGGACAAGACCAAGGCTACGAGAGCTCCAGCAGTGGCTTGGGCACAGTGTTTAACAGTCCTGTTTCTCAGCAGA
CACGGAGGAAATGGCCCATCAAGCGGCTAACATATTGGAGAACTGAAAGTGAGGAGGAAAATGCCTGTGTGGATGAGCAG
GACGGCTTAGGAGCATGCTTCAAGCAAGTTAAGTATATCTACTTATCCCTGGAATCTGATGATGATGATGACGACGACGA
CGACGACGACGACTCTGTTTTGAGATCTCTATCAAAGAAAAGGAAGGTATCGGATAACGTCCCATGGATTCCTAGGACAG
GTGAGATCCAAACACTCCTGGAGCAGGACCATCCTGTACTTGAGGGTACCAGAGTTACCTCCATTGAGATAGGCTTGGCT
ACCGCAGCTACAAAGCTATCACAGCAAGTGAACAACATGAAGCTCACTCTGATTAGTCCAGGAAAAAAAACAGCCAGTAA
ACAGAGACAATCAGACTTAAACCCATGTCCTCAAACTTCAGCTTTTCTGTTGCTTGATCCTTAA
ORF - retro_rnor_372 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.0 % |
| Parental protein coverage: | 80.55 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MASVPVYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGPSIMKKRRGSSK |
| MA.VPVYCLCR.PY.V..FMIECD.CQDWFHGSCVG.EEEKA.DID.YHCP.CEV..GPSIMKK...SSK | |
| Retrocopy | MALVPVYCLCRQPYNVNHFMIECDLCQDWFHGSCVGIEEEKAVDIDIYHCPDCEVIYGPSIMKKWPASSK |
| Parental | GHDNHKGKPLKTGSSMFIRELRGRTFDSSDEVILKPTGSQLTVEFLEENSFSVPILVLKKDGLGMTLPSP |
| .H...K..P.KTGS..FI..L.G.TFDSSDEVILKPTGSQLTVEFLEE.SFS.PILVLKK.GLGMTLP.. | |
| Retrocopy | EHEALKREPVKTGSPIFIHQLQGKTFDSSDEVILKPTGSQLTVEFLEESSFSIPILVLKKNGLGMTLPPT |
| Parental | SFTVRDVEHYVGSDKEIDVIDVARQADCKMKLGDFVKYYYSGKREKVLNVISLEFSDTRLSNLVETPKIV |
| SFTVRDVE.YVGSD.EIDVIDVA.QA..KM.LGDFVKYYYS..REKV.NVI.LEFS.TRLSN.VE.PKIV | |
| Retrocopy | SFTVRDVEQYVGSDREIDVIDVACQASSKMMLGDFVKYYYSRRREKVFNVINLEFSNTRLSNTVEMPKIV |
| Parental | RKLSWVENLWPEECVFERPNVQKYCLMSVRDSYTDFHIDFGGTSVWYHVLKGEKIFYLIRPTNANLTLFE |
| RKLSWVENLWPEEC.FERP.VQKYCLMSV..SYTDFHI.FGGTS.WYHVLKGEKIFYLI.PT.ANLTLF. | |
| Retrocopy | RKLSWVENLWPEECGFERPTVQKYCLMSVQNSYTDFHIEFGGTSIWYHVLKGEKIFYLIHPTDANLTLFK |
| Parental | CWSSSSNQNEMFFGDQVEKCYKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIE |
| CWS.SSNQ.EMFFGDQV.KCYKCSVKQGQTLFIPTGWI.AVLTPVDCLAFGGNFLHSLNIEMQLKAYE.E | |
| Retrocopy | CWSNSSNQKEMFFGDQVDKCYKCSVKQGQTLFIPTGWIYAVLTPVDCLAFGGNFLHSLNIEMQLKAYETE |
| Parental | KRLSTADLFKFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHEDEI |
| K.LSTA.LFKFP.FETICW.VGKH.LDIF.GLREN.R.PA.YLV.GGKALNLAF.AWTRKE.LPDHEDEI | |
| Retrocopy | KHLSTAHLFKFPSFETICWHVGKHMLDIFEGLRENGRYPAPYLVRGGKALNLAFQAWTRKEVLPDHEDEI |
| Parental | PETVRTVQLIKDLAREIRLVEDIFQQNVGKTSNIFGLQRIFPAGSIPLTRPAHSTSVSMSKLSLPSKNGS |
| P.TV.TVQLI.DLAREI.LVED..QQ...KTS.IFGLQ......S..L.R..HSTSVS.S.LSLPSK.GS | |
| Retrocopy | PKTVQTVQLIEDLAREICLVEDTSQQSIPKTSTIFGLQQHHTNPS-SLNRQTHSTSVSTSTLSLPSKSGS |
| Parental | KKKGLKPKDIFKKAERKGKQSSALGPAGQLSYNLMDPYSHQALKTGPSQKAKLNIGGACLNDSDDDSA-D |
| .KK..K.KDIFKK.E...K....LGP..Q.S.N.MD...HQ.LK.G.SQ....NI...CLNDSDDDS..D | |
| Retrocopy | EKKSPKYKDIFKKEEQTSKERPTLGPNDQHSCNFMDLNNHQELKVGFSQNVECNITSTCLNDSDDDSKFD |
| Parental | MDVDGSENPLALLMANGSTKRMKSVSKSRRAKIAKKVDSARLVAEQVMGDEFDLDSDDELQIDERLGKEK |
| ...DG.E....LLMANGSTKR.KS.S.S.RAKI.KK.D...LV.E..MGD.FDLD..DELQ...RLGK.K | |
| Retrocopy | KVCDGNESLVPLLMANGSTKRVKSLSNSWRAKITKKEDKSKLVEEKKMGDKFDLDTNDELQTEKRLGKVK |
| Parental | ANLLMRSKFPRKLPRAKPCSDPNRIREPGEVEFDIEEDYTTDEDMVEGVESKLGNGSGAGGILDLLKASR |
| ..L..RSK.P..LP..K.CS..N...EPGE.E.DI.E.Y..DE.M.EGVE.KL.NG....GILDLLKA.. | |
| Retrocopy | DSLVVRSKIPPNLPHVKFCSHQNQSCEPGETEIDIVENYKIDEGMMEGVEGKLKNGGESDGILDLLKARK |
| Parental | QVGGPDYAALTEAPASPSTQEAIQGMLCMANLQSSSSSPATSSLQAWWTGGQDRSSGSSSSGLGTVSNSP |
| QVGGP.Y..LT.AP...S..E..Q....MA.LQSSS.SPA.S.L...W.GGQD....SSSSGLGTV.NSP | |
| Retrocopy | QVGGPGYVVLTDAPDYSSSKENTQDTVFMAELQSSSPSPAPSTLHTLWSGGQDQGYESSSSGLGTVFNSP |
| Parental | ISQRTPGKRPIKRPAYWKNESEEEENASMDEQDSLGACFKDAEYIYPSLESDDDD |
| .SQ.T..K.PIKR..YW..ES.EEENA..DEQD.LGACFK...YIY.SLESDDDD | |
| Retrocopy | VSQQTRRKWPIKRLTYWRTES-EEENACVDEQDGLGACFKQVKYIYLSLESDDDD |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 33 .72 RPM |
| SRP017611_kidney | 0 .00 RPM | 34 .26 RPM |
| SRP017611_liver | 0 .00 RPM | 18 .22 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_372 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_372 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_372 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 | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000041229 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000002708 | 1 retrocopy |
retro_rnor_372 ,
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