RetrogeneDB ID: retro_mmus_3700

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:136701245..136701652(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080874
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lypla1
• Ensembl ID: ENSMUSG00000025903
• Aliases: Lypla1, Pla1a
• Description: lysophospholipase 1 [Source:MGI Symbol;Acc:MGI:1344588]

Sequence

>retro_mmus_3700
CCAGTTACATTAAATGAGAATTTGACTACGCCTTCTTTGTTTGATTGTATTGGACTTTAGCCACATTTTCAAGATGATGA
ATCTACAATTAAACAGACAACAGAAATGGGAAATCTCTGCTAGATCAAGAGATGAAGAATGGCATTCTGATAACAATGAT
TTTAGGAGGATCTTCCCAGGGACCTATCAGTGATACTAATAGAGTTACTTCTATTCTCCAGTGCCATGGAGATTGTGACC
CTTTAGTTCTCCTAAGGGTTGTTTCTCTTATTGTTCTACAATTAAAATCACTGGTAAAAGCAGCCAATGTAATCTTCAAA
GTCTATGGAGGCATGACACACAGTTCATGTCAGCAAGAAATGATGGATGTCAAACAATTTATTGATATACTCATATATCA
AATTAAT

Alignment

ORF - retro_mmus_3700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.59 %
• Parental protein coverage: 69.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVTLNMNMAMPSWFDIVGLSPDSQEDESGIKQAAE-TVKALIDQEVKNGIPSNRIILGGFSQGPINSANR
          PVTLN.N...PS.FD..GL.P..Q.DES.IKQ..E...K.L.DQE.KNGI.....ILGG.SQGPI...NR
Retrocopy PVTLNENLTTPSLFDCIGL*PHFQDDESTIKQTTE<NGKSLLDQEMKNGILIT-MILGGSSQGPISDTNR

Parental  DISVLQCHGDCDPLVPLMFGSLTVERLKALINPANVTFKIYEGMMHSSCQQEMMDVKHFIDKLLPPID
          ..S.LQCHGDCDPLV.L...SL.V..LK.L...ANV.FK.Y.GM.HSSCQQEMMDVK.FID.L...I.
Retrocopy VTSILQCHGDCDPLVLLRVVSLIVLQLKSLVKAANVIFKVYGGMTHSSCQQEMMDVKQFIDILIYQIN

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	20.07 RPM
SRP007412_cerebellum	0.00 RPM	17.11 RPM
SRP007412_heart	0.00 RPM	35.33 RPM
SRP007412_kidney	0.00 RPM	99.71 RPM
SRP007412_liver	0.00 RPM	92.03 RPM
SRP007412_testis	0.00 RPM	46.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3700 was not detected

EST

No EST(s) were mapped for retro_mmus_3700 retrocopy.

TSS

No TSS is located nearby retro_mmus_3700 retrocopy 5' end.

Lab

retro_mmus_3700 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3700 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006978	1 retrocopy	retro_cfam_523,
Equus caballus	ENSECAG00000016530	1 retrocopy	retro_ecab_238,
Echinops telfairi	ENSETEG00000001727	2 retrocopies	retro_etel_612, retro_etel_791,
Myotis lucifugus	ENSMLUG00000008208	1 retrocopy	retro_mluc_1683,
Macaca mulatta	ENSMMUG00000013157	3 retrocopies	retro_mmul_1734, retro_mmul_2459, retro_mmul_2474,
Mus musculus	ENSMUSG00000025903	1 retrocopy	retro_mmus_3700 ,
Nomascus leucogenys	ENSNLEG00000001027	4 retrocopies	retro_nleu_1137, retro_nleu_2015, retro_nleu_2817, retro_nleu_2869,
Oryctolagus cuniculus	ENSOCUG00000006751	3 retrocopies	retro_ocun_1510, retro_ocun_1623, retro_ocun_1679,
Otolemur garnettii	ENSOGAG00000003767	3 retrocopies	retro_ogar_1528, retro_ogar_1530, retro_ogar_1532,
Pteropus vampyrus	ENSPVAG00000005246	2 retrocopies	retro_pvam_224, retro_pvam_838,
Rattus norvegicus	ENSRNOG00000008320	3 retrocopies	retro_rnor_1747, retro_rnor_2612, retro_rnor_406,
Tupaia belangeri	ENSTBEG00000014207	8 retrocopies	retro_tbel_1839, retro_tbel_2439, retro_tbel_2478, retro_tbel_2907, retro_tbel_3127, retro_tbel_3466, retro_tbel_371, retro_tbel_4145,
Tursiops truncatus	ENSTTRG00000011836	3 retrocopies	retro_ttru_1643, retro_ttru_169, retro_ttru_291,