RetrogeneDB ID: retro_mmus_1157

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:120099447..120100332(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000095709
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ppp4r2
• Ensembl ID: ENSMUSG00000052144
• Aliases: Ppp4r2, BE691708, C230060M08Rik
• Description: protein phosphatase 4, regulatory subunit 2 [Source:MGI Symbol;Acc:MGI:3027896]

Sequence

>retro_mmus_1157
ATGGACGTCGAGAGGCTGCAGGAGGTGCTGAAAGATTTTGAGAAGAGAGGGAAAAAGGAAGTTTGTCCTGTACTGGATCA
GTTTCTCTGTCATGTAGCTAAAACTGGAGAAACAATGATTCAGTGGTCCCAATTTAAAGGCTATTTCATTTTCAAACTGG
AGAAAGTGATGGATGATTTCAGAACTTCAGCTCCTGAACCAAGAGGTCCTCCCAATCCTAATGTTGAATATATTCCCTTT
GATGAAATGAAGGAAAGAATACTGAAAATTGTCACTGGATTCAATGGTATCCCTTTTACTATTCAACGGCTATGTGAATT
GCTAACCGATCCAAGAAGAAATTATACAGGGACAGACAAGTTTCTCAGAGGAGTAGAGAAGAATGTGATGGTTGTTAGCT
GCGTTTGTCCATCCTCAGAGAAGAACAATTCTAATAGCTTAAATAGAATGAATGGTGTTATGTTTCCTGGAAACTCACCA
AACTATACTGACAGGTCTAATATAAACGGGCCTGGAACACCTAGGCCACTTAATCGACCAAAGCTTTCTTTGTCAGCCCC
CTTGACAACAAATGGTTTGCCTGAGAGCACAGATAGCAAAGATTCTGAGCTGCAGCTAAGTGAAGAGAAAGGCCACAGTG
ATTCTTCAGCCTCTGAATCAGAAGTTTCCTTACTGAGCCCTGTTAAAAATAAACATCCAGATGAAGATGCTGTGGAGTCT
GAGGAACATGAGGTGAAAAGACTGAAGTTTGACAAAGAAGGTGACGTCAGAGAGACAGCTAGCCAAATGGTGTCTGGTGA
AGTCTCTTCAGTTAGAGCAGAGGAAACGGAAACAGCAGCTCCCCCTCCTGACAAGGACAGAGAAAGTCGAACCAGGCAGC
ACTGT

Alignment

ORF - retro_mmus_1157 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.32 %
• Parental protein coverage: 70.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDVERLQEALKDFEKRGKKEVCPVLDQFLCHVAKTGETMIQWSQFKGYFIFKLEKVMDDFRTSAPEPRGP
          MDVERLQE.LKDFEKRGKKEVCPVLDQFLCHVAKTGETMIQWSQFKGYFIFKLEKVMDDFRTSAPEPRGP
Retrocopy MDVERLQEVLKDFEKRGKKEVCPVLDQFLCHVAKTGETMIQWSQFKGYFIFKLEKVMDDFRTSAPEPRGP

Parental  PNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVCPSSE
          PNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVCPSSE
Retrocopy PNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVCPSSE

Parental  KNNSNSLNRMNGVMFPGNSPNYTDRSNINGPGTPRPLNRPKLSLSAPLTTNGLPESTDSKDSELQLSEEK
          KNNSNSLNRMNGVMFPGNSPNYTDRSNINGPGTPRPLNRPKLSLSAPLTTNGLPESTDSKDSELQLSEEK
Retrocopy KNNSNSLNRMNGVMFPGNSPNYTDRSNINGPGTPRPLNRPKLSLSAPLTTNGLPESTDSKDSELQLSEEK

Parental  GHSDSSASESEVSLLSPVKNKHPDEDAVESEEHEVKRLKFDKEGDVRETASQTVSGEVSSVRAEETETAA
          GHSDSSASESEVSLLSPVKNKHPDEDAVESEEHEVKRLKFDKEGDVRETASQ.VSGEVSSVRAEETETAA
Retrocopy GHSDSSASESEVSLLSPVKNKHPDEDAVESEEHEVKRLKFDKEGDVRETASQMVSGEVSSVRAEETETAA

Parental  PPPDKDRESRTRQHC
          PPPDKDRESRTRQHC
Retrocopy PPPDKDRESRTRQHC

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	27.73 RPM
SRP007412_cerebellum	0.00 RPM	20.80 RPM
SRP007412_heart	0.00 RPM	14.16 RPM
SRP007412_kidney	0.00 RPM	21.77 RPM
SRP007412_liver	0.00 RPM	15.76 RPM
SRP007412_testis	0.00 RPM	30.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1157 was not detected

EST

No EST(s) were mapped for retro_mmus_1157 retrocopy.

TSS

No TSS is located nearby retro_mmus_1157 retrocopy 5' end.

Lab

retro_mmus_1157 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1157 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007954	3 retrocopies	retro_chof_1347, retro_chof_1914, retro_chof_2285,
Echinops telfairi	ENSETEG00000019946	2 retrocopies	retro_etel_1238, retro_etel_148,
Homo sapiens	ENSG00000163605	6 retrocopies	retro_hsap_2744, retro_hsap_2745, retro_hsap_2746, retro_hsap_2904, retro_hsap_3138, retro_hsap_3283,
Loxodonta africana	ENSLAFG00000000513	1 retrocopy	retro_lafr_603,
Macaca mulatta	ENSMMUG00000016959	1 retrocopy	retro_mmul_1224,
Mus musculus	ENSMUSG00000052144	3 retrocopies	retro_mmus_1068, retro_mmus_1157 , retro_mmus_3474,
Oryctolagus cuniculus	ENSOCUG00000006235	1 retrocopy	retro_ocun_292,
Pan troglodytes	ENSPTRG00000015108	5 retrocopies	retro_ptro_1855, retro_ptro_1856, retro_ptro_2121, retro_ptro_2220, retro_ptro_2974,