RetrogeneDB ID: retro_mmus_2564

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:43916752..43918228(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000093859
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Apex2
• Ensembl ID: ENSMUSG00000025269
• Aliases: Apex2, C430040P13Rik, ape2
• Description: apurinic/apyrimidinic endonuclease 2 [Source:MGI Symbol;Acc:MGI:1924872]

Sequence

>retro_mmus_2564
ATGTTATGCATGGTAAACTGGGACATCAATGGGATTCGGAGACCCCTGCAAGGTCTGGGATGCAAGGTGCCCAGCAACTG
TCCCACGGCCTTGAGATACATTTTAGAGGAGCTGGATGGCGATATTTTCTGTCTCCAGGAGACCAAAGTGAGCAGAGATG
CGCTGACGGAGCCCTTGGCTTTTGTTGAGGGCTATAACTCCTATTTCAGCTTCAGTCACAGCCGGAGTGGCTATCCTGGT
GTAGCTACTTTCTGTAAGGACAGTGTTACATCCGTGGCTGCTGAAGAAAGCCTGAGTGGTCAGTTTGCCACCCTGAACCG
GCATGTCGGTTGCTATGGAAACATGACCGCGTTCACCCAAGAGCAGCTACAGGCTCTGGATATCGAGGGCTGAGCTGTCC
TTACACCACAGCAAAAGGTCTTCACACAGGAAGAGAAGGGGAAGCCTTTGACCCTGATCAATGTGTACTGCCTGTGTACC
GATCCTAGGAACCCGGAGTGGCTGATCTTTAAGATGCATTTCTATCGCTTGCTGCAAATCCGAGCAGAAGCACTCCTGGC
AGCCGGCAGTCATGTGATAATCCTGGGGGGCATGAATATAGCGTACTGTCCCATTGACCACTGTGATGCTGGCGGTCTGG
GGTGCTTTGAAGAAGTCCTGGGTCGTAAGAGGATGGATGGCTTGCTTAGTAACCCGGAATACCAGGCTGGGTCCCATATA
GGACCTTTCATGGATAGCTATCTCTATTTCTATCCAAAACAGGAGAGGGCCTTTACCTGCTGGTCAGTGATCAGTAGTGT
CCGCAATCTCAACTATGGCACCCGACTTGACTACATACTGGGATACAGGACTCTAACTATAGACACTTTCCAAGATGCCT
TCCTGCTCCCTGAGATGATGGGCTCTGACCACTGCCCTGTGGAAGCTGTCTTGCATGTGTCCTGTATGCCAGCAAAGCAG
TGCCCAGCTCTGTGCACCCATTTTCTCCCCGAGTTTGCAGGTACCCAGCTCAAGATTCTTGGCTTCCTAGTCCCTTGTGA
ACAAGAACCTATGTGGTGGCAGCCAGTCCTGCAGCCCAGCAAACAAGTCCAGCTACAGAAAAAGAGAAAAGCCCACAGGC
ACTCATCCAGGCCTCGAAAGCATCAAGGTGGTCCCAGAAAACACCAGAAAAACCTGATGAGTTATTTTCAGCCTTCTGTT
AGCTTTTCCCAGACTTTTGGTGTGGAACTACCTAAGCTGCCTCTGGTGGGCACTCTTGTAACTCCAACAACTCTGGAAGG
GGATGTGATAGCCACAAAGAAGGATAAGCAGGCCAAGGTTTCTGAGGTCAGAAATGAGGAGGAGGCACAGACCTCATTCT
GGAAATCTGTGCTGAGTGGGCCCTCAGCCACGCCCCTCTGCAGAGGCCACAGGGAGCCATGTGTGATGTGGATTGTGAAA
AAAACAGGATCCAACCTGGGCCGCCATTTCTTTCTT

Alignment

ORF - retro_mmus_2564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 95.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRVVSWNINGIRSPLQGLACQEPSSCPTALRRVLDELDADIVCLQETKVTRDVLTEPLAIVEGYNSYFS
          ML..V.W.INGIR.PLQGL.C..PS.CPTALR..L.ELD.DI.CLQETKV.RD.LTEPLA.VEGYNSYFS
Retrocopy MLCMVNWDINGIRRPLQGLGCKVPSNCPTALRYILEELDGDIFCLQETKVSRDALTEPLAFVEGYNSYFS

Parental  FSRSRSGYSGVATFCKDSATPVAAEEGLSGVFATLNGDIGCYGNMDEFTQEELRVLDSEGRALLT-QHKI
          FS.SRSGY.GVATFCKDS.T.VAAEE.LSG.FATLN...GCYGNM..FTQE.L..LD.EG.A.LT.Q.K.
Retrocopy FSHSRSGYPGVATFCKDSVTSVAAEESLSGQFATLNRHVGCYGNMTAFTQEQLQALDIEG*AVLTPQQKV

Parental  RTLEGKEKTLTLINVYCPHADPGKPERLTFKMRFYRLLQMRAEALLAAGSHVIILGDLNTAHRPIDHCDA
          .T.E.K.K.LTLINVYC...DP..PE.L.FKM.FYRLLQ.RAEALLAAGSHVIILG..N.A..PIDHCDA
Retrocopy FTQEEKGKPLTLINVYCLCTDPRNPEWLIFKMHFYRLLQIRAEALLAAGSHVIILGGMNIAYCPIDHCDA

Parental  SSLECFEEDPGRKWMDGLLSNPGDEAGPHIGLFMDSYRYLHPKQQRAFTCWSVVSGARHLNYGSRLDYVL
          ..L.CFEE..GRK.MDGLLSNP...AG.HIG.FMDSY.Y..PKQ.RAFTCWSV.S..R.LNYG.RLDY.L
Retrocopy GGLGCFEEVLGRKRMDGLLSNPEYQAGSHIGPFMDSYLYFYPKQERAFTCWSVISSVRNLNYGTRLDYIL

Parental  GDRALVIDTFQASFLLPEVMGSDHCPVGAVLNVSCVPAKQCPALCTRFLPEFAGTQLKILRFLVPLEQEP
          G.R.L.IDTFQ..FLLPE.MGSDHCPV.AVL.VSC.PAKQCPALCT.FLPEFAGTQLKIL.FLVP.EQEP
Retrocopy GYRTLTIDTFQDAFLLPEMMGSDHCPVEAVLHVSCMPAKQCPALCTHFLPEFAGTQLKILGFLVPCEQEP

Parental  VREQQVLQPSHQIQAQRQPRKAFMHSTRLRKSQGGPKRKQKNLMSYFQPSSSLSQTSGVELPTLPLVGPL
          ...Q.VLQPS.Q.Q.Q...RKA..HS.R.RK.QGGP...QKNLMSYFQPS.S.SQT.GVELP.LPLVG.L
Retrocopy MWWQPVLQPSKQVQLQKK-RKAHRHSSRPRKHQGGPRKHQKNLMSYFQPSVSFSQTFGVELPKLPLVGTL

Parental  TTPKTAEEVATATMLEEKNKVPESKDEKGERTAFWKSMLSGPSPMPLCGGHREPCVMRTVKKTGPNFGRQ
          .TP.T.E....AT......KV.E...E....T.FWKS.LSGPS..PLC.GHREPCVM..VKKTG.N.GR.
Retrocopy VTPTTLEGDVIATKKDKQAKVSEVRNEEEAQTSFWKSVLSGPSATPLCRGHREPCVMWIVKKTGSNLGRH

Parental  FYM
          F..
Retrocopy FFL

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	5.28 RPM
SRP007412_cerebellum	0.00 RPM	5.17 RPM
SRP007412_heart	0.03 RPM	5.82 RPM
SRP007412_kidney	0.00 RPM	9.51 RPM
SRP007412_liver	0.00 RPM	6.80 RPM
SRP007412_testis	0.09 RPM	1.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2564 was not detected

EST

No EST(s) were mapped for retro_mmus_2564 retrocopy.

TSS

No TSS is located nearby retro_mmus_2564 retrocopy 5' end.

Lab

retro_mmus_2564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2564 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016584	1 retrocopy	retro_cjac_2967,
Myotis lucifugus	ENSMLUG00000016298	1 retrocopy	retro_mluc_287,
Mus musculus	ENSMUSG00000025269	1 retrocopy	retro_mmus_2564 ,
Mus musculus	ENSMUSG00000035960	2 retrocopies	retro_mmus_2027, retro_mmus_433,
Rattus norvegicus	ENSRNOG00000000166	1 retrocopy	retro_rnor_1061,