RetrogeneDB ID: retro_pabe_2535

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:86108998..86110263(-)
• Located in intron of: None

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_2535
ATTCGCTGTCAGGAATTGAAACACAACATTGGTGGAGGAGAACGGTTTGATTCTTTGACAGATCTTGTGGAGCATTACAA
GAAGAATCCAATGGTGGAAACATTGGGTACAGTACTACAACTCAAGCAGCCCCCTAACATGACTCGTATAAATGCTGCTG
AAATAGAAAGCAGAGTTCGAGAACTAAGCAAATTAGCTGAGACCACAGATAAAGTCAAACAAGGCTTTTGGAAAGAATTT
GAGACACTGCAACAACAGGAGTGCAAACTTCTCTACAACTGAAAAGAGGGTCAAAGGCAAGAAAATAAAAACAAAAATAG
ATATTAAAAACATCCTGCCCTTTGATCATACCAAGGTTATTCTACATGACGGGATCCCAATGAGCCTGTTTCAGATTACA
TCAATGCAAATATCATCATGCCTGAATTTGAAACCAAGTGCAACAATTCAAAGCCCAAAAAGAGTTACATTGACACACAA
AGCTGCCTGCAAAACACAGTGAATGACTTTTGGCGGATGGTGTTCCAAGAAAACTCCAGAGCGATTGTCATGACAATGAA
AGAAGTGGAGAGAAGAAAGAGTAAATGTGTCAAATACTGGTCTGATGAGTATGCGCTAAAAGAATATGACGTCATTCGTG
TTAGGAACCTCAAAGAAAGCGCCGCTCACGACTATACGCTAAGAGAACTTAAACTTTCAAAGGTTGGACAAGGGAATACG
GAGAGAACAGTCTGGCAATACCATTTTCGAACCCGGCTGGACCACGGAGTGCTCAGCAACCCCGGGGGTGTGCCGGACCT
CCTGGAGAAGGTGCACCATAAGCAGGAGAGCATCATGGATGCAGGGCCGTTCGTGGTGCACTGCAGTGCTGGAATTGGCC
GGACAGGGACGTTCATTGTGATTGATATTCTTATTGACATCATCAGAGAGAAGGTGTTGACTGCAACATTGATGTTCCCC
AAACCACCCAGATGGTGTGGTCTACGAGGTCAGGGATGGTCCAGACGGAAGCACGGTACCGATTTATCTATATGGCGGTC
CAGCATTATATGGAAACACTACAGCGCAAGATTGAACAAAAGCAGAAATGCAAGAGGAAAGGGCACGAATATATAAATAT
TAAGTATCCTCTAGCAGACCAGACGAGTGGAAATCAGAGCCCCCTGCCGCCTTGTACTCCAAAGCCACCCTGTGCAGAAA
TGAGAGAAAACAGTGCTAGAGTCTATGAAAACGTGGGCCTGATGCAACAGCAGAAAACTTTCAGA

Alignment

ORF - retro_pabe_2535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.71 %
• Parental protein coverage: 71.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTD
          IRCQELK...GGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQP.N.TRINAAEIESRVRELSKLAETTD
Retrocopy IRCQELKHNIGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPPNMTRINAAEIESRVRELSKLAETTD

Parental  -KVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDG-DPNEPVSDYINANI
          .K....F..................K...............ILPFDHT.V.LHDG.DPNEPVSDYINANI
Retrocopy >KSNKAFGKNLRHCNNRSANFSTTEKRVKGKXXXXXXXXXXILPFDHTKVILHDG<DPNEPVSDYINANI

Parental  IMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKE
          IMPEFETKCNNSKPKKSYI.TQ.CLQNTVNDFWRMVFQENSR.IVMT.KEVER.KSKCVKYW.DEYALKE
Retrocopy IMPEFETKCNNSKPKKSYIDTQSCLQNTVNDFWRMVFQENSRAIVMTMKEVERRKSKCVKYWSDEYALKE

Parental  YGVMRVRNVKESAAHDYTLRELKLSK-GQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESI
          Y.V.RVRN.KESAAHDYTLRELKLSK.GQGNTERTVWQYHFRT..DHGV.S.PGGV.D.LE.VHHKQESI
Retrocopy YDVIRVRNLKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTRLDHGVLSNPGGVPDLLEKVHHKQESI

Parental  MDAGPVVVHCSAGIGRTGTFIVIDILIDIIREK-GVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAV
          MDAGP.VVHCSAGIGRTGTFIVIDILIDIIREK.GVDC.IDVP.T.QMV.S.RSGMVQTEA.YRFIYMAV
Retrocopy MDAGPFVVHCSAGIGRTGTFIVIDILIDIIREK<GVDCNIDVPQTTQMVWSTRSGMVQTEARYRFIYMAV

Parental  QHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPCTPTPPCAEMREDSARVYENVGLMQQ
          QHY.ETLQR.IE..QK.KRKGHEY.NIKY.LADQTSG.QSPLPPCTP.PPCAEMRE.SARVYENVGLMQQ
Retrocopy QHYMETLQRKIEQKQKCKRKGHEYINIKYPLADQTSGNQSPLPPCTPKPPCAEMRENSARVYENVGLMQQ

Parental  QKSFR
          QK.FR
Retrocopy QKTFR

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	0.83 RPM	68.95 RPM
SRP007412_cerebellum	0.24 RPM	26.75 RPM
SRP007412_heart	0.15 RPM	25.26 RPM
SRP007412_kidney	0.20 RPM	16.21 RPM
SRP007412_liver	0.15 RPM	7.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2535 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2535 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,