RetrogeneDB ID: retro_pabe_2825

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5_random:14801330..14802542(-)
• 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_2825
AAGGAGCTGAAATACGACGTTGGTGGAGGAGAACGGTTTGATTCTTTGACAGATCTTGAAGAACATTACAAGAAGAATCT
CATGGTGGAAACACTGGGTACAGTAGTACAACTCAAGCATCCCCTTAACATGACTCATATAAATGCTGCTGAAATAGAAA
GCAGAGTTCAGGAACTAAGCAAATTAGCTGAGACCACAGATAAAGTCAAACAAGGCTTTTGGGAAAAATTTGAGACACTA
CAACAGGAGTGCAAACTTCTCTACAGCCGAAAAGAGGGTCAAAGGCAAGAAAACACAAACAGAAATAGATATAAAACCAT
CCTACCCTTTGATCATATATGGGTTGTCCTACACGACGGTGATCCCAATGAGCCTGTTTCAGATTACATCAATGAAAATA
TCATCATGCCTGAATTTGAAACCAAGTGCAACAATTCAAAGTCCTAAAAGTGTTACATTGCCACACAAGGCTGCCTGCAA
AACACAGTGAATGACTTTTGGCAGATGAAGTTCCAAGAAAACTCCCGAGTGATTGTCATGACAATAAAAGAAGTGGAGAG
AGGAAAGAGTAAATGTGTCAAATACTGGCCTGATGAGTATGCTCTAAAAGAATATGGCATCATGCGTGTTAGGAACGTCA
AAGAAAGCGCAGCTCATGATTATACGCTAAGAGAACTTAAACTTTCAAAGGTTGGACAAGGGAATATGGAGAGAATGGTC
TGGCAATACCACTTTGGGACCTGGCCGGACCATGGAGTGCCCAGCGACCCCAGAGGCGTGCTGGACTTCCTAGAGGAGGT
GTACCATAAGCAGGAGAGCATCACGGATGCAGGGCTGGTCGTGGTGCACTGCAGTGCTGGAATTGGCCTGACAGGGACGT
TCATTGTTATTGATATTCTTATTGACATTGTCAGAGAGAAAGGTGTTGACTGCAACATTGATGTTCCCAAAACCATCCAG
ATGGTGCGGTCTCAGAGGTCAGGGATGGTCCAGACAGAAGCATAGTACCGATTCATCTGTATGGCAGTCCAGCATTATAT
TGAAACACTGCAGCTCAGGATTGAAGAAGAGCAGAAAAGCAAGAGGAAAGGGCACAAATATACAGATATTAAATATTCTC
TAGTAGACCAGACAAGTGAAGATCAAAACGCCCTCTTGCCTTGTATTCCAACGCCACCCTGTGCAGAAATGAGAGAAGAC
AGTGCTAGAGTC

Alignment

ORF - retro_pabe_2825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 68.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVK
          .ELKYDVGGGERFDSLTDL.EHYKKN.MVETLGTV.QLK.PLN.T.INAAEIESRV.ELSKLAETTDKVK
Retrocopy KELKYDVGGGERFDSLTDLEEHYKKNLMVETLGTVVQLKHPLNMTHINAAEIESRVQELSKLAETTDKVK

Parental  QGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEF
          QGFWE.FETLQQ.ECKLLYSRKEGQRQEN.N.NRYK.ILPFDH..VVLHDGDPNEPVSDYIN.NIIMPEF
Retrocopy QGFWEKFETLQQ-ECKLLYSRKEGQRQENTNRNRYKTILPFDHIWVVLHDGDPNEPVSDYINENIIMPEF

Parental  ETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMR
          ETKCNNSK..K.YIATQGCLQNTVNDFW.M.FQENSRVIVMT.KEVERGKSKCVKYWPDEYALKEYG.MR
Retrocopy ETKCNNSKS*KCYIATQGCLQNTVNDFWQMKFQENSRVIVMTIKEVERGKSKCVKYWPDEYALKEYGIMR

Parental  VRNVKESAAHDYTLRELKLSK-GQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGP
          VRNVKESAAHDYTLRELKLSK.GQGN.ER.VWQYHF.TWPDHGVPSDP.GVLDFLEEV.HKQESI.DAG.
Retrocopy VRNVKESAAHDYTLRELKLSKVGQGNMERMVWQYHFGTWPDHGVPSDPRGVLDFLEEVYHKQESITDAGL

Parental  VVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIET
          VVVHCSAGIG.TGTFIVIDILIDI.REKGVDC.IDVPKTIQMVRSQRSGMVQTEA.YRFI.MAVQHYIET
Retrocopy VVVHCSAGIGLTGTFIVIDILIDIVREKGVDCNIDVPKTIQMVRSQRSGMVQTEA*YRFICMAVQHYIET

Parental  LQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPCTPTPPCAEMREDSARV
          LQ.RIEEEQKSKRKGH.YT.IKYSL.DQTS.DQ..L.PC.PTPPCAEMREDSARV
Retrocopy LQLRIEEEQKSKRKGHKYTDIKYSLVDQTSEDQNALLPCIPTPPCAEMREDSARV

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	0.00 RPM	26.75 RPM
SRP007412_heart	0.00 RPM	25.26 RPM
SRP007412_kidney	0.00 RPM	16.21 RPM
SRP007412_liver	0.00 RPM	7.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2825 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2825 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,