RetrogeneDB ID: retro_mmul_1877

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:47001686..47002619(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000000864
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTPN11
• Ensembl ID: ENSMMUG00000013253
• Aliases: PTPN11, SHP2
• Description: tyrosine-protein phosphatase non-receptor type 11 [Source:RefSeq peptide;Acc:NP_001248038]

Sequence

>retro_mmul_1877
CTGCCCTTTGATCATACCCGGGTTGTTGTTCTTGACGGTGATCCCAATGAGCCTGTTTCAGATTACATCAATGCAAATAT
CATCATGCCTGAATTTGAAACCAAGTGCAACAATTCGAAGCCCAAAAAGAGTTACACTGCCACACAAGGCTGCCTGCAAA
ACACAGTGAGTGACTTTTGGTGGATGGTGTTCCAAGAAAACTCCAGAGTGATTGTCATGACAATGAAAGAAGTGGAGAGA
GGAAAGAGTAAACGTGTCAAATACTGGCCTGATGAGTATGCTCTAAAAGAATATGGCGTCATGCCTGTTAGGAACATCAA
AGAAAGCACCACTCATGACTATACGCTAAGAGAACTTAAACTTTCAAAAGTTGGACAAGGGAATATGGAGAGAACAGTCT
GGCAATACCACTTTCGGACCTGGCCGGATCACGGAGTGCTCAGCAACCCCGGGGGCGTGCTGGACCTCCTGGAGAAGGTG
CACCATAAGCAGGAGAGCATCATGGATGCAGGGCCGGTCGTGGTGCACTGCAGTGCTGGAATTGGCCGGACAGGGACTTT
CATTGTGATCGATAGTCTTATCGACATCATCAGAGAGGAAGGTGTTGACTGCAACATTGATGTTCCCCAAACCATCCAGA
TGGTGTGGTCCAAGAGGTCAGGGATGGTCCAGACAGAAGCACGGTACCGATTTATCTATATGGCAGTCCAGCGTTATATT
GAAACACTACAGCGCAGGATTGAACAAAAGCAGAAAAGCAAGAGGAAAGGGAACGAATATACGAATATTAAGTATTCTCT
AGCAGACCAGACGAGTGGAGACCAGAACCCCCTCCTGCCTTGTACTCCAATGCCACCCTGTGCAGAAATGAGAAAAGACA
GGGCTAGAATCTATGAAAACGTGGGCCTGATGCAACAGCAGAAAAGTTTCAGA

Alignment

ORF - retro_mmul_1877 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.39 %
• Parental protein coverage: 52.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRV
          LPFDHTRVV..DGDPNEPVSDYINANIIMPEFETKCNNSKPKKSY.ATQGCLQNTV.DFW.MVFQENSRV
Retrocopy LPFDHTRVVVLDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYTATQGCLQNTVSDFWWMVFQENSRV

Parental  IVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRT
          IVMT.KEVERGKSK.VKYWPDEYALKEYGVM.VRN.KES..HDYTLRELKLSKVGQGN.ERTVWQYHFRT
Retrocopy IVMTMKEVERGKSKRVKYWPDEYALKEYGVMPVRNIKESTTHDYTLRELKLSKVGQGNMERTVWQYHFRT

Parental  WPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPK
          WPDHGV.S.PGGVLD.LE.VHHKQESIMDAGPVVVHCSAGIGRTGTFIVID.LIDIIRE.GVDC.IDVP.
Retrocopy WPDHGVLSNPGGVLDLLEKVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDSLIDIIREEGVDCNIDVPQ

Parental  TIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPP
          TIQMV.S.RSGMVQTEA.YRFIYMAVQ.YIETLQRRIE..QKSKRKG.EYTNIKYSLADQTSGDQ.PL.P
Retrocopy TIQMVWSKRSGMVQTEARYRFIYMAVQRYIETLQRRIEQKQKSKRKGNEYTNIKYSLADQTSGDQNPLLP

Parental  CTPTPPCAEMREDSARVYENVGLMQQQKSFR
          CTP.PPCAEMR.D.AR.YENVGLMQQQKSFR
Retrocopy CTPMPPCAEMRKDRARIYENVGLMQQQKSFR

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	0.22 RPM	106.78 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	85.36 RPM
SRP007412_cerebellum	0.32 RPM	55.47 RPM
SRP007412_heart	0.00 RPM	48.93 RPM
SRP007412_kidney	0.00 RPM	34.62 RPM
SRP007412_liver	0.00 RPM	10.25 RPM
SRP007412_testis	0.00 RPM	8.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1877 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1877 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1877 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3061

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012464	1 retrocopy	retro_cjac_1051,
Homo sapiens	ENSG00000179295	5 retrocopies	retro_hsap_2823, retro_hsap_3061, retro_hsap_3302, retro_hsap_3670, retro_hsap_4062,
Gorilla gorilla	ENSGGOG00000010689	1 retrocopy	retro_ggor_1962,
Macaca mulatta	ENSMMUG00000013253	4 retrocopies	retro_mmul_1501, retro_mmul_1792, retro_mmul_1877 , retro_mmul_2345,
Monodelphis domestica	ENSMODG00000003120	1 retrocopy	retro_mdom_516,
Nomascus leucogenys	ENSNLEG00000000078	5 retrocopies	retro_nleu_1200, retro_nleu_1360, retro_nleu_1654, retro_nleu_522, retro_nleu_561,
Pongo abelii	ENSPPYG00000004976	4 retrocopies	retro_pabe_2205, retro_pabe_2535, retro_pabe_2825, retro_pabe_3336,