RetrogeneDB ID: retro_mmus_3474

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:75233412..75234309(+)
• Located in intron of: ENSMUSG00000031196

Retrocopy information

• Ensembl ID: ENSMUSG00000083736
• 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_3474
GACAAGTTTCTCAGAGGAGTAGAGAAGAATGTGATGGTTGTTAGCTGCGTTTGTCCATCCTCAGAGAAGAACAATTCTAA
TAGCTTAAATAGAATGAATGGTGTTATGTTTCCTGGAAACTCACCAAACTATACTGACAGGTCTAATATAAACGGGCCTG
GAACACCTAGGCCACTTAATCGACCAAAGCTTTCTTTGTCAGCCCCCTTGACAACAAATGGTTTGCCTGAGAGCACAGAT
AGCAAAGATTCTGAGCTGCAGCTAAGTGAAGAGAAAGGCCACAGTGATTCTTCAGCCTCTGAATCAGAAGTTTCCTTACT
GAGCCCTGTTAAAAATAAACATCCAGATGAAGATGCTGTGGAGTCTGAGGAACATGAGGTGAAAAGACTGAAGTTTGACA
AAGAAGGTGACGTCAGAGAGACAGCTAGCCAAACGGTGTCTGGTGAAGTCTCTTCAGTTAGAGCAGAGGAAACGGAAACA
GCAATTCCCCCTCCTGACAAGGACAGAGAAAGTCGAACCAGGCAGCACTGTACAGAAGAGGAGGAGGAGGAGGAAGAAGA
AGAGGAAGAGGAGGAGGAAGAATCGTTTATGACACCAAGAGAAATGGTCCCAGAAAGAAAAAATCAAGAAAAGGAATCTG
ATGACACCTTAACTGTGAATGAAGAGACTTCAGAGGAGAGCCATCAGATGGAAGGCTCTGGTGTGTCTCCAGCTCAGACA
GACTCCACTTCAGAAAGGAGTGACAGTGCAGGGGCCTCAAGGAGTGGCTCTGACTGCCTGGAGACACAGGAGTCAGGAGG
GCCTCCTTCCAGTAAGACCGGAGAAAGTGTGTCAGTGCCGTCGTCCATGGAGAATGAGGAAGCCACAGAAGTCACAGATG
ACCCAATGGAACAAGAC

Alignment

ORF - retro_mmus_3474 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.98 %
• Parental protein coverage: 71.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DKFLRGVEKNVMVVSCVCPSSEKNNSNSLNRMNGVMFPGNSPNYTDRSNINGPGTPRPLNRPKLSLSAPL
          DKFLRGVEKNVMVVSCVCPSSEKNNSNSLNRMNGVMFPGNSPNYTDRSNINGPGTPRPLNRPKLSLSAPL
Retrocopy DKFLRGVEKNVMVVSCVCPSSEKNNSNSLNRMNGVMFPGNSPNYTDRSNINGPGTPRPLNRPKLSLSAPL

Parental  TTNGLPESTDSKDSELQLSEEKGHSDSSASESEVSLLSPVKNKHPDEDAVESEEHEVKRLKFDKEGDVRE
          TTNGLPESTDSKDSELQLSEEKGHSDSSASESEVSLLSPVKNKHPDEDAVESEEHEVKRLKFDKEGDVRE
Retrocopy TTNGLPESTDSKDSELQLSEEKGHSDSSASESEVSLLSPVKNKHPDEDAVESEEHEVKRLKFDKEGDVRE

Parental  TASQTVSGEVSSVRAEETETAAPPPDKDRESRTRQHCTEEEEEEEEEEEEEEEESFMTPREMVPERKNQE
          TASQTVSGEVSSVRAEETETA.PPPDKDRESRTRQHC.................SFMTPREMVPERKNQE
Retrocopy TASQTVSGEVSSVRAEETETAIPPPDKDRESRTRQHCXXXXXXXXXXXXXXXXXSFMTPREMVPERKNQE

Parental  KESDDALTVNEETSEESHQMEGSGVSPAQTDSTSERSDSAGASRSGSDCLETQESGGPPSSKTGESVSVP
          KESDD.LTVNEETSEESHQMEGSGVSPAQTDSTSERSDSAGASRSGSDCLETQESGGPPSSKTGESVSVP
Retrocopy KESDDTLTVNEETSEESHQMEGSGVSPAQTDSTSERSDSAGASRSGSDCLETQESGGPPSSKTGESVSVP

Parental  SSMESEEAAEVTDDPMEQD
          SSME.EEA.EVTDDPMEQD
Retrocopy SSMENEEATEVTDDPMEQD

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	0.02 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 activity may be related with retro_mmus_3474 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	X:75232984..75233488

EST

2 EST(s) were mapped to retro_mmus_3474 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG061121	75233493	75233613	100	120	0	120
CN529636	75233561	75233704	100	143	0	143

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_158012	553 libraries	434 libraries	83 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_3474 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3474 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,