RetrogeneDB ID: retro_mmus_2027

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:39558156..39558733(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084285
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Apex1
• Ensembl ID: ENSMUSG00000035960
• Aliases: Apex1, APE, Apex, HAP1, Ref-1
• Description: apurinic/apyrimidinic endonuclease 1 [Source:MGI Symbol;Acc:MGI:88042]

Sequence

>retro_mmus_2027
ATGCCAAAATGGGGGGAGAGAGTGGGCTCCTGAAGATGGGTTAGATTCCAAGTTGGGGCCAGACACCAAAAAGAGTAAGG
AGGCAGCAAAGTAAAATGAGAAGGCTGCAGGAGTGGTTCTATCCTGTATGAGGACCCTCCAGATCAGAAAACCTCATCCA
GTGGCAAATCGGCCACACTCAAGATATGCTTCTGGAATGTGGATGGGCTTGGAGCCTGGATTACAAAGAAAGGCTTGTAT
TGAGTAAAGAAAGAAGTGCCAGATACCATGTGCCTCCAAGAGATCAAATGCTCAAAGAGCAAACTCTTGGCTGAACTTCA
AGAGCTGCCTGGACTCACCAATCAGTACTAGTCAGCTTCATAAGACAAAGAAGGATATAGAAGGTGTGGCCATTCAACTT
TCCCACCAGTGCCCACTCAAAAGTCTCTATGGCATTGGTGAAGAACATGATCAAGAAGGTGGGGTGATTGTGACTGAATT
TGACTTCTTTGTCCTGGTAACAGCCTATGTTCCCAATGCAGGCAAGGGTCTGATAAGACTGGAATACTGGCAGCATTGGG
GTGAAGCCTTCACCAAG

Alignment

ORF - retro_mmus_2027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.56 %
• Parental protein coverage: 60.88 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPKRGKKA-AADDGEEPKSEPETKKSKGAAKKTEKEAAG-EGPVLYEDPPDQKTSPSGKSATLKICSWNV
          MPK.G....A..DG...K..P.TKKSK.AAK..EK.AAG..G..LYEDPPDQKTS.SGKSATLKIC.WNV
Retrocopy MPKWGERV>APEDGLDSKLGPDTKKSKEAAK*NEK-AAG<SGSILYEDPPDQKTSSSGKSATLKICFWNV

Parental  DGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLTHQYWSAPSDKEGY-SGVGL-LSRQ
          DGL.AWI.KKGL..VK.E.PD..CLQE.KCS..KL.AELQELPGLT.QY.SA..DKEGY..GV...LS.Q
Retrocopy DGLGAWITKKGLY*VKKEVPDTMCLQEIKCSKSKLLAELQELPGLTNQY*SAS*DKEGY>EGVAIQLSHQ

Parental  CPLKVSYGIGEEEHDQEGRVIVAEFESFVLVTAYVPNAGRGLVRLEYRQRWDEAFRK
          CPLK..YGIG.EEHDQEG.VIV.EF..FVLVTAYVPNAG.GL.RLEY.Q.W.EAF.K
Retrocopy CPLKSLYGIG-EEHDQEGGVIVTEFDFFVLVTAYVPNAGKGLIRLEYWQHWGEAFTK

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	3.11 RPM
SRP007412_cerebellum	0.00 RPM	2.04 RPM
SRP007412_heart	0.00 RPM	2.71 RPM
SRP007412_kidney	0.00 RPM	2.44 RPM
SRP007412_liver	0.00 RPM	3.66 RPM
SRP007412_testis	0.00 RPM	4.44 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2027 was not detected

EST

No EST(s) were mapped for retro_mmus_2027 retrocopy.

TSS

No TSS is located nearby retro_mmus_2027 retrocopy 5' end.

Lab

retro_mmus_2027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2027 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002745	1 retrocopy	retro_btau_1729,
Echinops telfairi	ENSETEG00000004855	1 retrocopy	retro_etel_1392,
Loxodonta africana	ENSLAFG00000021872	1 retrocopy	retro_lafr_948,
Mus musculus	ENSMUSG00000025269	1 retrocopy	retro_mmus_2564,
Mus musculus	ENSMUSG00000035960	2 retrocopies	retro_mmus_2027 , retro_mmus_433,
Otolemur garnettii	ENSOGAG00000013335	3 retrocopies	retro_ogar_1284, retro_ogar_2145, retro_ogar_3243,
Rattus norvegicus	ENSRNOG00000009663	1 retrocopy	retro_rnor_2971,
Ictidomys tridecemlineatus	ENSSTOG00000010096	1 retrocopy	retro_itri_1560,
Tupaia belangeri	ENSTBEG00000006405	1 retrocopy	retro_tbel_3409,