RetrogeneDB ID: retro_mmus_106

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:33065099..33067826(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000023350
• Aliases: 4921501E09Rik, PHF8
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Phf8
• Ensembl ID: ENSMUSG00000041229
• Aliases: Phf8, 9830141C09Rik, mKIAA1111
• Description: PHD finger protein 8 [Source:MGI Symbol;Acc:MGI:2444341]

Sequence

>retro_mmus_106
ATGGCCTTGGTGCCTGTGTATTGTCTTTGTCGACAGCCTTATAATGTGAACCACTTCATGATTGAGTGCGGCCTGTGCCA
GGACTGGTTTCATGGTAGCTGTGTTGGGATTGAAGAAGAAAACGCTGTTGACATTGACATCTACCACTGCCCAGACTGTG
AGGCTGTATTTGGGCCTTCCATTATGAAAAACTGGCATGGATCGCCTAGAGGGCATGATGCTCTCAAGAGGAAGCCATTG
ATGACTGGGAGCCCTACCTCTATTCACCAAATCCAGGGTAGGATTTTTGAAAGCTCTGACAAAGTGATTTTGAAGCCCAC
AGGAAGTCATTTAACAGTAGAATTTCTGCTAGAAAGTAGCTTCAGCATACCTATCCTTGTCTTGAAGAAGGATGGGTTGG
GGATGACACTTCCACCGACATCATTCACTGTCAGAGATGTTGAGCAATATGTTGGTTCTGACAGAGAGGTTGATGTGATT
GATGTAGCCTGTCAGGCTAGCAGCAAGATGATGTTGGGAGATTTTGTGAAATATTATTACAGCAGGAAGAGGGAAAAGAC
CTTTAATGTTATTAATTTGGAATTCTCTAATACTGGGCTTTCTAATATAGTAGAGATGCCCAAGATAGTTCGTAAGCTTT
CCTGGGTTGAAAACTTATGGCCAGAAGATTGCGGCTTTGAGAGACCCAATGTACAGAAGTATTGCCTTATGAGTATGCAG
AATAGCTATACAGATTTTCACATTGAATTTGGTGGCACTTCAGCCTGGTACCATGTAGTTAAGGGTGAGAAGATCTTCTA
TCTGATCCGCCCAACAGATGCTAACCTGACTCTTTTTGAGTGTTGGAGCAACTCTTCTAACCAAAAGGAAATATTCTTTG
GTGACCAGGTAGACAGATGTTACAAGTGTTCTGTGAAGCAAGGACAGACACTTTTCATTCCTACAGGATGGATCTATGCT
GTGCTGACCCCAGTGGATTGCCTAGCATTTGGGGGAAACTTCTTACACAGTTTAAACATTGAAATGCAGCTCAAAGTCTA
TGAGATTGAGAAGCATCTGTGTACAACAGACCTCTTCAAGTTTCCAAGCTTTGAGACCATCTGTTGGCATGTGGGGAAAC
ACATCCTGGACATCTTTAAAGGTTTACGGGAGAATGGGAGATGTCCTGCATCCTTCTTGGTCCATGGTGGTAAAGCTCTA
AACTTGGCCTTTCAAGCCTGGACAAGGAAAGAAGTTCTGCCTAACCGTGATAATGAGATCCCAAAGACAGTGCAGACCAT
ACAGCTCATTGAAGATCTGGCTTGGGAAATTCATCTGGTTGAAGATAATTTCCAACAGAACATCCCAAAGACAAGTTCTA
CCTTTAAGTTCCAGCAGCTCCATACCAATTCCTCTTCCTTAACTAGGCAAGCTCATCCCACTTCAGTATCCAAGTCTAAA
TTATCACTGCCCTCCAAAAATGGTTCAGAAAAGAAAAGCCCAAAGTATAAAGACACCTTTAAGAAGGAAGAACAAATGAG
CAAGGAGAGTTCAGCTCTGGGGCCTAATTATCAACATAGCTGTAATTTCATGGATCTAAATAATGATCAACAATGGAAGG
TAGGCTGTCTCCAAAACGTAGAGTTTAACATCACTAGTACTTGTTTGAATGATTCAGATGATAACTCAAAACATGACAAA
GCCTTCAATGGGAATGAGAGCCTGGTGCCTCTGTTGATGGCTAATGGCAATACGAAGAGGGAAAAGAGCTTGTCCGAATC
TTGGCAAGCCAAAATCACAAAGAAGGAAGATACATCAAGGTTGATGAAAGAACAAGCGATGGTAGACACATTTGACTTGG
ATTTAAATGATGAGCTACAGATTGAAAAGGGATTAGGTAAAGAGAAAGTGAGTCTGGTAGTAAGACCAAAAATTCCTCCA
AGTTTGCCCCATGTGAAGCTTTGCTCTGACCAAAACCAAAGTCATGATCCAGGGGAAACTGAGATCACCATTGTAGAGAA
CTATAAAATAGATAAGGAAATGGTGGAAGAGGTTGAAGGCAAGTTTAAGAATGGAAGTGAATCTGGTGGAACTATTGATC
CACTAAAGGCCAAGAAACAGGTGGGTGGACCTGGCTGTGTTATCCTCACTGATGACCCAAACTCTTCCAGCAATAAGAAG
GACATTCAGGACACTGTGTGCATGTCTGATTTGCAGTCTTCTCCTCCTTCACAAGCTCCCTCCAGCCTTCAGGCATTTTG
GAGTGGGGGACAAGACCAAGGCAACAAAAGCCCTAGCAGTGTCTTGGGCACAGTGTCTGACAGTCCTGTTTCTCGGCGTA
CCCCAAGGAAATGGCCCATCAAGCGGCTAGCATACTGGAGAAATGAAAGTGAGGCGGGAAATGCTTGTGTAGATGAACAG
GGCAGCTTAGGAGCATGCTTCAAGGAAGCTAAGTATATCTTCTTATCCCTGGAATCTGATGACGACGACGATGATGATGA
TGATGACGACGATGACAACAACCCTGCTTTGAGAGTTCTACCAAAGAAAAGGAAGATATCAGATAATGCCCCAAGGATTC
CTAGGGCAGATGAGATCCCAACACTACCAAAGCAGGACCATTCTGTGCCTGAGGGTAACAGAGTTGGCTCCATTGAGATA
GACTGGACTACAGCAGCTACAAAGCTGGCACAGGAGGTGAACAACATGAAGCTCACTCTCACTAGTCCAGGAAAAAGCAG
CCAATAA

Alignment

ORF - retro_mmus_106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.61 %
• 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..FMIEC..CQDWFHGSCVG.EEE.A.DID.YHCP.CE...GPSIMK...GS..
Retrocopy MALVPVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGPSIMKNWHGSPR

Parental  GHDNHKGKPLKTGSSMFIRELRGRTFDSSDEVILKPTGSQLTVEFLEENSFSVPILVLKKDGLGMTLPSP
          GHD..K.KPL.TGS...I....GR.F.SSD.VILKPTGS.LTVEFL.E.SFS.PILVLKKDGLGMTLP..
Retrocopy GHDALKRKPLMTGSPTSIHQIQGRIFESSDKVILKPTGSHLTVEFLLESSFSIPILVLKKDGLGMTLPPT

Parental  SFTVRDVEHYVGSDKEIDVIDVARQADCKMKLGDFVKYYYSGKREKVLNVISLEFSDTRLSNLVETPRIV
          SFTVRDVE.YVGSD.E.DVIDVA.QA..KM.LGDFVKYYYS.KREK..NVI.LEFS.T.LSN.VE.P.IV
Retrocopy SFTVRDVEQYVGSDREVDVIDVACQASSKMMLGDFVKYYYSRKREKTFNVINLEFSNTGLSNIVEMPKIV

Parental  RKLSWVENLWPEECVFERPNVQKYCLMSVRDSYTDFHIDFGGTSVWYHVLKGEKIFYLIRPTNANLTLFE
          RKLSWVENLWPE.C.FERPNVQKYCLMS...SYTDFHI.FGGTS.WYHV.KGEKIFYLIRPT.ANLTLFE
Retrocopy RKLSWVENLWPEDCGFERPNVQKYCLMSMQNSYTDFHIEFGGTSAWYHVVKGEKIFYLIRPTDANLTLFE

Parental  CWSSSSNQNEMFFGDQVEKCYKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIE
          CWS.SSNQ.E.FFGDQV..CYKCSVKQGQTLFIPTGWI.AVLTPVDCLAFGGNFLHSLNIEMQLK.YEIE
Retrocopy CWSNSSNQKEIFFGDQVDRCYKCSVKQGQTLFIPTGWIYAVLTPVDCLAFGGNFLHSLNIEMQLKVYEIE

Parental  KRLSTADLFKFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTKKEALPDHEDEI
          K.L.T.DLFKFP.FETICW.VGKHILDIF.GLREN.R.PAS.LVHGGKALNLAF.AWT.KE.LP....EI
Retrocopy KHLCTTDLFKFPSFETICWHVGKHILDIFKGLRENGRCPASFLVHGGKALNLAFQAWTRKEVLPNRDNEI

Parental  PETVRTVQLIKDLAREIRLVEDIFQQNVGKTSNIFGLQRIFPAGSIPLTKPAHSTSVSMSKLSLPSKNGS
          P.TV.T.QLI.DLA.EI.LVED.FQQN..KTS..F..Q......S..LT..AH.TSVS.SKLSLPSKNGS
Retrocopy PKTVQTIQLIEDLAWEIHLVEDNFQQNIPKTSSTFKFQQLH-TNSSSLTRQAHPTSVSKSKLSLPSKNGS

Parental  KKKGLKPKDIFKKAERKGKQSSALGPAGQLSYNLMDPYSHQALKTGPSQKAKFNMSGTSLNDSDDDSA-D
          .KK..K.KD.FKK.E...K.SSALGP..Q.S.N.MD....Q..K.G..Q...FN...T.LNDSDD.S..D
Retrocopy EKKSPKYKDTFKKEEQMSKESSALGPNYQHSCNFMDLNNDQQWKVGCLQNVEFNITSTCLNDSDDNSKHD

Parental  MDLDGSENPLALLMANGSTKRMKSVSKSRRAKIAKKVDSARLVAEQVMGDEFDLDSDDELQIDERLGKEK
          ....G.E....LLMANG.TKR.KS.S.S..AKI.KK.D..RL..EQ.M.D.FDLD..DELQI...LGKEK
Retrocopy KAFNGNESLVPLLMANGNTKREKSLSESWQAKITKKEDTSRLMKEQAMVDTFDLDLNDELQIEKGLGKEK

Parental  ANLLIRSKFPRKLPRAKPCSDPNRIREPGEVEFDIEEDYTTDEDMVEGVESKLGNGSGAGGILDLLKASR
          ..L..R.K.P..LP..K.CSD.N....PGE.E..I.E.Y..D..MVE.VE.K..NGS..GG..D.LKA..
Retrocopy VSLVVRPKIPPSLPHVKLCSDQNQSHDPGETEITIVENYKIDKEMVEEVEGKFKNGSESGGTIDPLKAKK

Parental  QVGGPDYAALTEAPASPSTQEAIQGMLCMANLQSSSSSPATSSLQAWWTGGQERSSGSSSSGLGTVSSSP
          QVGGP....LT..P.S.S....IQ...CM..LQSS..S.A.SSLQA.W.GGQ.....S.SS.LGTVS.SP
Retrocopy QVGGPGCVILTDDPNSSSNKKDIQDTVCMSDLQSSPPSQAPSSLQAFWSGGQDQGNKSPSSVLGTVSDSP

Parental  ASQRTPGKRPIKRPAYWKNESEEEENASLDEQDSLGACFKDAEYIYPSLESDDDD
          .S.RTP.K.PIKR.AYW.NES.E..NA..DEQ.SLGACFK.A.YI..SLESDDDD
Retrocopy VSRRTPRKWPIKRLAYWRNES-EAGNACVDEQGSLGACFKEAKYIFLSLESDDDD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.02 RPM	34.37 RPM
SRP007412_cerebellum	0.00 RPM	46.63 RPM
SRP007412_heart	0.00 RPM	20.33 RPM
SRP007412_kidney	0.00 RPM	29.14 RPM
SRP007412_liver	0.00 RPM	25.45 RPM
SRP007412_testis	30.05 RPM	46.56 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_106 was not detected

EST

No EST(s) were mapped for retro_mmus_106 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_52459	1065 libraries	5 libraries	1 library	1 library	0 libraries
TSS #2	TSS_52460	1067 libraries	1 library	2 libraries	1 library	1 library

The graphical summary, for retro_mmus_106 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_106 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	retro_mmus_106 ,
Rattus norvegicus	ENSRNOG00000002708	1 retrocopy	retro_rnor_372,