RetrogeneDB ID: retro_mmus_2368

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:80440367..80440881(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082555
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pla2g12a
• Ensembl ID: ENSMUSG00000027999
• Aliases: Pla2g12a, 2310004B05Rik, GXII, GXII-1, GXII-1-PLA2, Pla2g12, Rossy, mGXII-1
• Description: phospholipase A2, group XIIA [Source:MGI Symbol;Acc:MGI:1913600]

Sequence

>retro_mmus_2368
AAGCCTGTTCCTCAGCCCCACCCAGGGCCTGTACTCCTGCTCCTGCTGGCCACTACATCTGGTTACAAACAGGTCCAGAT
AACCACCTGGAGGGTCACACTTAAGAGAATCTGCAATGTTATGCATAGTATCTACATGTTCCTCGAGGTAGTGCTGGACC
TACTGGGTGAAAATGACAGGTTTTGCCAGTACGACTGCAGTGAAGAATCAAAGCCTTTTCCATGCTAAAGATATAATCCT
TCCCAACCAAACGGAGAGTATTCCCATGGTTTGGTATTCAACAGAAAAATGACACTTCTTTCCTGACAAAGTGCTGAAAC
CAAAATTACAGGTGTTATGATACCTGTGGTAAAAGCAAGAACAATTTGACAATGAGTTCTAATACTGCCTCTCCAAGATC
TTCTGAGATGCACAGAAGACTCTAGGCCTTGCTCAAAATGTTCAGGAGAAGGAAGATAGGATGGAAACACATCCCAAGTC
CACATCTCACTTTCTCACTCTAAAGCCTGTGCTC

Alignment

ORF - retro_mmus_2368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.45 %
• Parental protein coverage: 89.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPAPARSPALLLLLLLATARGQEQDQTTDWRATLKTIRNGIHKIDTYLNAALDLLGGEDGLCQYKCSDGS
          .P.P...P...LLLLLAT..G..Q.Q.T.WR.TLK.I.N..H.I...L...LDLLG..D..CQY.CS..S
Retrocopy KPVPQPHPGPVLLLLLATTSGYKQVQITTWRVTLKRICNVMHSIYMFLEVVLDLLGENDRFCQYDCSEES

Parental  KPVPRYGYKPSPPNGCGS-PLFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDC-DEEFQYCLSKICRDV
          KP.P...Y.PS.PNG..S.P.FG.........LTKC.NQ..RCY.TCGKSKN...D.EF.YCLSKI..D.
Retrocopy KPFPC*RYNPSQPNGEYS<PWFGIQQKNDTSFLTKC*NQNYRCYDTCGKSKNNL<DNEF*YCLSKIF*DA

Parental  QKTLGLSQNVQACETTVELLFDSVIH-LGCKPYL
          QKTLGL.QNVQ..E...E....S..H.L..KP.L
Retrocopy QKTLGLAQNVQEKEDRMETHPKSTSHFLTLKPVL

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	10.84 RPM
SRP007412_cerebellum	0.00 RPM	9.99 RPM
SRP007412_heart	0.00 RPM	34.31 RPM
SRP007412_kidney	0.00 RPM	17.11 RPM
SRP007412_liver	0.00 RPM	8.77 RPM
SRP007412_testis	0.00 RPM	15.73 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2368 was not detected

EST

No EST(s) were mapped for retro_mmus_2368 retrocopy.

TSS

No TSS is located nearby retro_mmus_2368 retrocopy 5' end.

Lab

retro_mmus_2368 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2368 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172, retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242, retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368 ,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30, retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623, retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,