RetrogeneDB ID: retro_mmus_3000

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:14227436..14228477(-)
• Located in intron of: ENSMUSG00000070810

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Rpap3
• Ensembl ID: ENSMUSG00000022466
• Aliases: Rpap3, 2310042P20Rik, D15Ertd682e
• Description: RNA polymerase II associated protein 3 [Source:MGI Symbol;Acc:MGI:1277218]

Sequence

>retro_mmus_3000
ATTTTTGATGAGCTTAACAAAGAAGATAGCACCACACCATTCCATGTATCTGTGTCCTAGGAGTCAGAATCAGAAGAAGA
CAGCATTTGTGTGGATTCCCGAAGCTCTTGCTCTAAAAGAAAAAGATAATAGGTACTTCAAGCAAGGAAAATACTACGAA
GCCATTGAATGCTCCACGAAAGGCGTGGATATCTATCCCTATAATCCCATGTTGACAACAAACAGGGCATCCACTTACTT
AAGACTGAAAAAATTTGCTATTGCTGAGTCTGACTGTAATTTGGCCATTGCATTAAACAGGAGTCACACCAAGGCTTACA
GCAGACAAAGTGCTGCTCGGTTTTGCTCAGCAAAAATTGGAAGATACCAGAAAAGATTATGAGAAAGTGTTAGAACTGGA
ACCAGACAACTTTGGAGCAACAAATGAACTTAGGAAAACTGACCAGGTTTTAACATCCAAAGAGAACTCATGTCCCAAAG
AAGCTGCTGCCATGATTAAGCCAGGTGCAGCCGAGGAAAACCCACTGAAGATCAACGGGGCAGGCAGAAGGCCATTGCAG
ACAAAGACCTGGGCAATGGATTTTTCAAACAGAGGAAATATGAGCAAGCAACTGAACTCTACAACCCGAGGGATAGCAGC
AGACAGCACCAACACCCTATTTCCATCTAACAGAGTGATGGCCATCTCAAGATTCAGAAATATGAATCTGAAAGAGACTG
CACACAAGCTATCTTACTATATGGTTCACATTCAAAAGTGTTTGCCAGAAGTGGAACCGCAAGGACATTTTTGGTAAAGA
TGAATGTGGCCAAGCAAGATTTTGAAACTGTTTTACTTTAGAACCAGGAAATTAACAAGCAGTGACTGAGCTTTCCAGAA
GTTAAAAGGAATTAATTGAGAAAGGACATTGGAGTGATGTCTTTCTTGGCTACACACTGAGACACAGTGTGGTGAAACCT
GTAGATAATCCTCATTTTAGGTTACCTAAAGCACTCAAGAAGGTTTTTATTGAAGAAACTGGCAATTTGAAAGACACTGT
T

Alignment

ORF - retro_mmus_3000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.55 %
• Parental protein coverage: 52.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ILDELDKEDST-HDS--LSQESESDEDGIRVDSQKALVLKEKGNKYFKQGKYDEAIECYTKGMDADPYNP
          I.DEL.KEDST.H.S..L...S........V....AL.LKEK.N.YFKQGKY.EAIEC.TKG.D..PYNP
Retrocopy IFDELNKEDST>HHSMYLCPRSQNQKKTAFVWIPEALALKEKDNRYFKQGKYYEAIECSTKGVDIYPYNP

Parental  VLPTNRASAYFRLKKFAVAESDCNLAIALSRTYTKAYARRGAAR-FALQKLEDARKDYEKVLELEPDNFE
          .L.TNRAS.Y.RLKKFA.AESDCNLAIAL.R..TKAY.R..AAR.FA.QKLED.RKDYEKVLELEPDNF.
Retrocopy MLTTNRASTYLRLKKFAIAESDCNLAIALNRSHTKAYSRQSAAR>FAQQKLEDTRKDYEKVLELEPDNFG

Parental  ATNELRKINQALTSKENSGPGAAAAAESKPAAGE-SKPTGGQQGRQKAIAEKDLGNGFFKEGKYEQAIEC
          ATNELRK..Q.LTSKENS.P...AAA..KP.A.E..KPT..Q.GRQKAIA.KDLGNGFFK..KYEQA.E.
Retrocopy ATNELRKTDQVLTSKENSCP-KEAAAMIKPGAAE<GKPTEDQRGRQKAIADKDLGNGFFKQRKYEQATEL

Parental  Y-TRGIAADRTNALLPANRAMA-YLKIQRYEEAERDCTQAIVLDGSYSKAFARRGTARTFLGKINEAKQD
          Y.TRGIAAD.TN.L.P.NR.MA..LKIQ.Y.E.ERDCTQAI.L.GS.SK.FAR.GTARTFL.K.N.AKQD
Retrocopy Y>TRGIAADSTNTLFPSNRVMA<HLKIQKY-ESERDCTQAILLYGSHSKVFARSGTARTFLVKMNVAKQD

Parental  FETVLL-LEPGNKQAATELSRIKKELIEKGHWDDVFLDSTQRHHVVKAVDNPPRGSPKALKKVFIEETGN
          FETVLL.LEPGN.QA.TELSR..KELIEKGHW.DVFL..T.RH.VVK.VDNP....PKALKKVFIEETGN
Retrocopy FETVLL<LEPGN*QAVTELSRS*KELIEKGHWSDVFLGYTLRHSVVKPVDNPHFRLPKALKKVFIEETGN

Parental  LIETV
          L..TV
Retrocopy LKDTV

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	0.00 RPM	18.15 RPM
SRP007412_cerebellum	0.00 RPM	18.11 RPM
SRP007412_heart	0.00 RPM	12.76 RPM
SRP007412_kidney	0.00 RPM	15.13 RPM
SRP007412_liver	0.00 RPM	6.55 RPM
SRP007412_testis	0.00 RPM	10.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3000 was not detected

EST

No EST(s) were mapped for retro_mmus_3000 retrocopy.

TSS

No TSS is located nearby retro_mmus_3000 retrocopy 5' end.

Lab

retro_mmus_3000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3000 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022466	2 retrocopies	retro_mmus_3000 , retro_mmus_424,