RetrogeneDB ID: retro_pabe_3336

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:60386729..60387813(-)
• Located in intron of: ENSPPYG00000018610

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN11
• Ensembl ID: ENSPPYG00000004976
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 11 [Source:HGNC Symbol;Acc:9644]

Sequence

>retro_pabe_3336
CTAAGCAAATTAGCTGAAGAACACAATAAAAGTCAAACAAGCTTTTGGGAAGAATTTGAGACACTACAACAACAGGAGTG
CAAACTTCTCTACAGCCGAAAAGAGGGTCAAAGGCAAGAAAACAAAAACAAAAAATAGATATAAAAACATCCTGCCCTTT
GATCACACCAGGGTTGTCCTACACGATGGTGATCCCAATGAGCCTGTTTCAGATGACATCAATGCAAATATCATCATGCC
CGAATTTGAAATCAAGTGTAACAATTCAAAGCCCAAAAAGAGTTACATTGCCACACAAGGCTGCCTGCAAAACATGGTGA
ACGACTTTTGGCGGATGGTATTCCAAGAAAACTCCCGAGTGATTGTCATGACAACGAAACAAGTGGAGAGCGGAAAGAGT
AAATGTGTCAAATACTGGCCTGGTGAGTATGCTCTAAAAGAATATGGCATTATGCGTGTTAGGAATGTCAGAGAAAGCGC
CGCTCACAACTATATGCTAAGAGAACTTAAACTTTCAAAGGTTGGACAAGTGAATAAGGAGAGAATGGTCTGGCAATACC
ACTTTTGGACCTGGCCGGACCACGGAATGCCCATTGACCCCAGGGGTGTGCTGGACTTCCTGGAGGAGGTGCACCATAAG
CAGGAACGCATCATGCATGCAAGGCCAGTCGTGGTGCACTGCAGTGCTGGAATTGGCCGGACAGGGACATATGTTGTGAT
TGATATTCTGATTGACATCAACAGAGAGAAAGGTGTTGACTGTGACATTGACGTTCTCAAAACCATCCAGATGGTGCAGT
CTCAGAGGTCAGGGATGGTCCAGACAGAAGCACAGTACCGATTTATCTATATGGCGGTCCAGCATTATACTGAAACACTA
CAGCGCAGGACTGAAGAAGAGCAGAAAAGCAAGAGGAAAGGGCATGAATATACAAATATTAAGTATTCTCTAGCGGACCA
GACGAGTGGAGATCAGAGCCCCCTCCCGCCTTGTACTCCAACTCCACGCTGTGCAGAAATGAGAGAAGACAGTGCTAGAG
TGTAAGAAAACGTGGGCCTGACGCAACAGCAGAAGAGTTTCAGA

Alignment

ORF - retro_pabe_3336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.22 %
• Parental protein coverage: 60.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSKLAE-TTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPV
          LSKLAE..T.KVKQ.F..................K...............ILPFDHTRVVLHDGDPNEPV
Retrocopy LSKLAE>NTIKVKQAFGKNLRHYNNRSANFSTAEKRVKGKXXXXXXXXXXILPFDHTRVVLHDGDPNEPV

Parental  SDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYW
          SD.INANIIMPEFE.KCNNSKPKKSYIATQGCLQN.VNDFWRMVFQENSRVIVMTTK.VE.GKSKCVKYW
Retrocopy SDDINANIIMPEFEIKCNNSKPKKSYIATQGCLQNMVNDFWRMVFQENSRVIVMTTKQVESGKSKCVKYW

Parental  PDEYALKEYGVMRVRNVKESAAHDYTLRELKLSK-GQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEE
          P.EYALKEYG.MRVRNV.ESAAH.Y.LRELKLSK.GQ.N.ER.VWQYHF.TWPDHG.P.DP.GVLDFLEE
Retrocopy PGEYALKEYGIMRVRNVRESAAHNYMLRELKLSKVGQVNKERMVWQYHFWTWPDHGMPIDPRGVLDFLEE

Parental  VHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQY
          VHHKQE.IM.A.PVVVHCSAGIGRTGT..VIDILIDI.REKGVDCDIDV.KTIQMV.SQRSGMVQTEAQY
Retrocopy VHHKQERIMHARPVVVHCSAGIGRTGTYVVIDILIDINREKGVDCDIDVLKTIQMVQSQRSGMVQTEAQY

Parental  RFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPCTPTPPCAEMREDSARVYE
          RFIYMAVQHY.ETLQRR.EEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPCTPTP.CAEMREDSARV.E
Retrocopy RFIYMAVQHYTETLQRRTEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPCTPTPRCAEMREDSARV*E

Parental  NVGLMQQQKSFR
          NVGL.QQQKSFR
Retrocopy NVGLTQQQKSFR

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_prefrontal_cortex	0.11 RPM	68.95 RPM
SRP007412_cerebellum	0.12 RPM	26.75 RPM
SRP007412_heart	0.15 RPM	25.26 RPM
SRP007412_kidney	0.07 RPM	16.21 RPM
SRP007412_liver	0.06 RPM	7.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3336 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3336 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 23 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,
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 ,
Pongo abelii	ENSPPYG00000008983	3 retrocopies	retro_pabe_1077, retro_pabe_1144, retro_pabe_989,