RetrogeneDB ID: retro_mmul_1501

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:27227934..27228861(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_1501
CCCTTTGATCATAGGGTTGTCCTACACAACGGTGATCCCAGTGAGCCTGTTTCAGATTACATCAATGCAACTATAACCGT
GCCTAAATTTGAAATCAAGTGCAACAATTCAAAGCCCAAAAAGAGTTACATTGCCACACAAGGCTGCCTGCAAAACACGG
TGAACGACTTTTGGCGGATGGTGTTCCAAGAAGACTCCCAGGTGATTGTCATGACAAGGAAAGAAATGGAGAGAGGAAAG
AGTAAATATGTCAAATATTGGCCTGATGAGTATGCTCTCAAAGCATATGGCGTCATGCGTGGTAGGAACGTCAAAGAAAG
CACCACTCATGACTATAAGCTAAGAGAACTTGAACTTTCAAAGGTTGGACAAGGGACTATGGAGAGAATGGTCTGGCAAT
ACCACTCTTGGAGCTGGCTGGGCCACGGAGTGCCCAGCGACCCCAGGGGCATGCTGGACTTCCTGGAGGAGGTGCACCAT
AAGCAGGGGAGCATCATGGATGCAGGGCCGTTTGTGGTGCACTGCAGTGCTGGCATTGGCCGGACAGGGACCTTCATTGT
GACTGATATTTTTATTGACATCATCAGAGAGAAAGGTGTTGACTGCAACATTGATGTTCCCAAAACCATCCACGTGGTGT
AGTCTCAGAGGTCAGGAATGGTCCAGACAGAAGCACAGTACCGATTTATCTATATGGCAGTCCAGTATTATATTGAAACA
CTACAGCGCAGGATTGAGGAAGAGCAGAAAAGCAAGAGGAAAGGGCACGAATATACAAATATTAAGTATTCTCTAGTGGA
CCAGATGAGTGGAGATCACAGCCCCCTCCTGCCTTATACTTCAGTGCCACCCTGTGCAGAAATGAGAGAAGACAGTGCTA
GAGTCTATGAAAATGTGGGCCTGGTGCAACAGCAGAAACGTTTAAGA

Alignment

ORF - retro_mmul_1501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.52 %
• Parental protein coverage: 52.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVI
          PFDH.RVVLH.GDP.EPVSDYINA.I..P.FE.KCNNSKPKKSYIATQGCLQNTVNDFWRMVFQE.S.VI
Retrocopy PFDH-RVVLHNGDPSEPVSDYINATITVPKFEIKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQEDSQVI

Parental  VMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTW
          VMT.KE.ERGKSK.VKYWPDEYALK.YGVMR.RNVKES..HDY.LREL.LSKVGQG..ER.VWQYH...W
Retrocopy VMTRKEMERGKSKYVKYWPDEYALKAYGVMRGRNVKESTTHDYKLRELELSKVGQGTMERMVWQYHSWSW

Parental  PDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKT
          ..HGVPSDP.G.LDFLEEVHHKQ.SIMDAGP.VVHCSAGIGRTGTFIV.DI.IDIIREKGVDC.IDVPKT
Retrocopy LGHGVPSDPRGMLDFLEEVHHKQGSIMDAGPFVVHCSAGIGRTGTFIVTDIFIDIIREKGVDCNIDVPKT

Parental  IQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPC
          I..V.SQRSGMVQTEAQYRFIYMAVQ.YIETLQRRIEEEQKSKRKGHEYTNIKYSL.DQ.SGD.SPL.P.
Retrocopy IHVV*SQRSGMVQTEAQYRFIYMAVQYYIETLQRRIEEEQKSKRKGHEYTNIKYSLVDQMSGDHSPLLPY

Parental  TPTPPCAEMREDSARVYENVGLMQQQKSFR
          T..PPCAEMREDSARVYENVGL.QQQK..R
Retrocopy TSVPPCAEMREDSARVYENVGLVQQQKRLR

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	0.06 RPM	55.47 RPM
SRP007412_heart	0.06 RPM	48.93 RPM
SRP007412_kidney	0.12 RPM	34.62 RPM
SRP007412_liver	0.00 RPM	10.25 RPM
SRP007412_testis	0.04 RPM	8.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1501 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1501 has 0 orthologous retrocopies within eutheria group .

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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,