RetrogeneDB ID: retro_mmus_3727

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:166482192..166483602(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000085880
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam154a
• Ensembl ID: ENSMUSG00000028492
• Aliases: Fam154a, 4930500O09Rik
• Description: family with sequence similarity 154, member A [Source:MGI Symbol;Acc:MGI:1923061]

Sequence

>retro_mmus_3727
AGGAAGTGCATCTGTGACCTTTGCTCCTGCGGCAGGCATCACTGCCCACATCTCCCTACCAAGATTTATGAGAAGACAGA
GAAACCATGTTTTTTCTCCGAATACTCGGAGAAGTATTCTACCTATCATTCTTATATGCCCCAAGAGTCCTTCAAACCCA
AGGTGGAGTACCAGAAAGTAGCTATACCAATGGAAGGACTGTCCACAACAAAGAGAGACTTTGGGGCTTACAACATAGTA
CCGGTGAAACACCATCTTCCCGAGAAGGTCACTCCAATCCAAGATGAAATGGATTTCCTCACAACGTATAATCAACACTA
CAACTATTGCCCTGCCACTCGAGCGAGCCCCATCAAACCTCGAGACAACAGGCATCAATGTAATGACAAAATGGAGTATG
AGCCTACGTACAAAGCTGATTATTTACCTTGGAACCAACAAAAAAGATCTTTGATTCATCCACCACAATCATACCGTCCT
CCGTCCTGTAGGTTTGATCATAGAACCACACACCAGGACGATTATCCCATGAAAAGTCCTGTGGATACTGTGAATTACAA
ACCTCCACCTGGGCCCAAGCTCTCCAACCTCCCCCTGGAGAATATGACAAGCTACAGATCGAGCTATGTGGCCCATCCTG
TGGAGAAGCGGTGTGTGTATGAGGGAGAGAAATATAAACCATGTGAAATTCCTTTTGATGGCCTTACCACCCACAGAGAT
TCCTACAAGGGTTTGATGGGGGAACCTGCCAAGAGCTGGAAACCTGTACCAAATCACTCTGGGCTAGGTATACCTTTTGC
AACCGACACTGAATTTCGAGAAAATTTTCAAGCTTGGCCAACACCTAAGATTGTCCCCAAAGAGCCCATTCCCTACATCC
CTCCTGAAGGAAAGATGGATCTTCTGACAACTGTGCAAGCCAACTATAAATGCCCCAATGGCGCTCCTGCTCAGTCCTGC
CGGCCAGTCATCCACTTGAAGAAGAGTGAGCGATTTGAAAGCTCTACCACCAACAGAGAGGATTATAAACACTGGGACAT
CATCCCTAGAGAGCCAATCAAACCTGCTCCCCAGCTGAAATTCCCTGATGAGCCTATGGATTACATGACCACCAATCGTG
CCCACTACGTGCCTCATGCACCAGTCAATACCAAAAGCTGCAAGCCAACCTGGTCCGGCCCTCGTGTAAACATCCCGTTA
GAAGGTCAGACCACCTACTCTTCTAATTTTACTCCTAAGGAAATTCAAAGGTGCCCAGCTTCATTCTCTGAACCCCCTGG
CTACATCTTTGAAGAGGTGGATGCTGTAGGGCACAGGATGTACAGGCCGGCTTCCAGAGCAGCTTCTCATGAGAGCAACC
ATCTTGGCTTTGGTGATGTGTAAAGAATTGGCACTCCCAGCCTGTCATTG

Alignment

ORF - retro_mmus_3727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.99 %
• Parental protein coverage: 98.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTCICNLCSCGRHRCPHLPTKIYDKTEKTRLLSEYTENYPIYQSYLPRNSFKPEWCYRKPSAPMEGLTTC
          R.CIC.LCSCGRH.CPHLPTKIY.KTEK....SEY.E.Y..Y.SY.P..SFKP...Y.K...PMEGL.T.
Retrocopy RKCICDLCSCGRHHCPHLPTKIYEKTEKPCFFSEYSEKYSTYHSYMPQESFKPKVEYQKVAIPMEGLSTT

Parental  RRDFGLHKMLPVTFHQPDTYVPSQETMDLLTTYKHDFNYLPTCPVGLIKPRDSKFPNGDKIMQYLPTYKV
          .RDFG.....PV..H.P....P.Q..MD.LTTY....NY.P......IKPRD......DK.M.Y.PTYK.
Retrocopy KRDFGAYNIVPVKHHLPEKVTPIQDEMDFLTTYNQHYNYCPATRASPIKPRDNRHQCNDK-MEYEPTYKA

Parental  DYLPWNQPRRELLRPPHKYRPESSKFENRTTHQDDYTMKGLVTTVSCKPPSKSKIYNIPLEDLTNYKMSY
          DYLPWNQ..R.L..PP..YRP.S..F..RTTHQDDY.MK..V.TV..KPP...K..N.PLE..T.Y..SY
Retrocopy DYLPWNQQKRSLIHPPQSYRPPSCRFDHRTTHQDDYPMKSPVDTVNYKPPPGPKLSNLPLENMTSYRSSY

Parental  VPHPVEKRFVKEAEKYIPCDIPFENLTTHKESYRGLLGEPAKSTKPPAKFPVHDAPFTNTTEVQEKFQAW
          V.HPVEKR.V.E.EKY.PC.IPF..LTTH..SY.GL.GEPAKS.KP.........PF...TE..E.FQAW
Retrocopy VAHPVEKRCVYEGEKYKPCEIPFDGLTTHRDSYKGLMGEPAKSWKPVPNHSGLGIPFATDTEFRENFQAW

Parental  PTPQMVPKAPVVYVPPEEKMDLLTTVQTHYKYLKGSPAITCRPVPSIKKSKCFESSTTTKDDFKQWAAVN
          PTP..VPK.P..Y.PPE.KMDLLTTVQ..YK...G.PA..CRPV...KKS..FESSTT...D.K.W....
Retrocopy PTPKIVPKEPIPYIPPEGKMDLLTTVQANYKCPNGAPAQSCRPVIHLKKSERFESSTTNREDYKHWDIIP

Parental  TKPIRPTLHLSLPAEPLDCQTTTKTCFVAHPPIITENYKPPWVGLRRNIPVEGQTTYSINFTPKDLGKCP
          ..PI.P...L..P.EP.D..TT.....V.H.P..T...KP.W.G.R.NIP.EGQTTYS.NFTPK....CP
Retrocopy REPIKPAPQLKFPDEPMDYMTTNRAHYVPHAPVNTKSCKPTWSGPRVNIPLEGQTTYSSNFTPKEIQRCP

Parental  ASYMEPPGYIFEEVDSMGHKIYRSISQTGSRQNSSISICDTEKPGQKELEV
          AS..EPPGYIFEEVD..GH..YR..S...S.........D....G...L..
Retrocopy ASFSEPPGYIFEEVDAVGHRMYRPASRAASHESNHLGFGDV*RIGTPSLSL

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	0.12 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.02 RPM	0.04 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	12.58 RPM	63.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3727 was not detected

EST

No EST(s) were mapped for retro_mmus_3727 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_156360	1065 libraries	4 libraries	1 library	1 library	1 library
TSS #2	TSS_156361	1059 libraries	9 libraries	1 library	1 library	2 libraries

The graphical summary, for retro_mmus_3727 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_3727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3727 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_20

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028492	1 retrocopy	retro_mmus_3727 ,
Rattus norvegicus	ENSRNOG00000048197	1 retrocopy	retro_rnor_20,