RetrogeneDB ID: retro_pabe_2205

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:25788137..25789076(+)
• 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_2205
CAAAACATCCTGCCCTTTGATCATAGGGTTGTCCTACACAACGGTGATCCCAGTGAGACTGTTTCAGATTACATCAATGC
AAATATCATCGTGCCTGAATTTGAAACCAAGTGCAACAATTTGAAGCCCAAAAAGAGTTACATTGCCACACAAGGCTGCC
TGCAAAACACCGCGAACGACTTTTGGTGGATAGTGTTCCAAGAAAACTCCCAGGTGATTGTCATGACAATGAAAGAAGTG
GAGAGAGGAAAGAGTAAATGTGTCAAATACTGGCCTGATGAGTATGCTGTAAAAGAATATGGCATCATGCATGTTAGGAA
CGTCAAAGAAAGCGCCACTCATGACTATAAGCTAAGAGAACTTAAACTTTCAAAGATTGGAAAAGGGAATATGGAGAGAA
TGGTCTGGCAATACCACTTTTGGACCTGGCTGTACCACGGAGTGCCCTGCGACTCCAAGGGTATGCTGCACTTCCTGGAC
GAAGTGCACCGTAAGCAGGATAGCATCATGGATGCAGGGCTGGTTGTGGTGCACTGCAGTGCTGGCATTGGCCAGACAGG
GACGTTCATTGTGATTGATATTCTTATTGACATCATCAGAGAGAAAGGTGTTGACTGCGAAATTGATGTTCCCAAAACCA
TCCAGATGGTGCAGTCTCAGAGGTCAGAGATGGTCCAGACAGAAGCACAGTACCGATTTATCTATATGGCGGTCCAGCAT
CATATTGAAACACTACAGCGCAGGATTGAGGAAGAGCAGAAAAGCAAGAGGAAAGGGCACGAATGTACAAATATTAAGTA
TTCTCTAGTGGACCAGACGAGTGGAGATCAGAGCCCCCTCCTGCCTTATACTCCAATGCCACCCTGTGCAGAAATGAGAG
AAGAGAGTGCTAGAGTCTATGAAAATGTGGGCCTGATGCAACAGCAGAAACATTTAAGA

Alignment

ORF - retro_pabe_2205 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.35 %
• Parental protein coverage: 52.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQEN
          .NILPFDH.RVVLH.GDP.E.VSDYINANII.PEFETKCNN.KPKKSYIATQGCLQNT.NDFW..VFQEN
Retrocopy QNILPFDH-RVVLHNGDPSETVSDYINANIIVPEFETKCNNLKPKKSYIATQGCLQNTANDFWWIVFQEN

Parental  SRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSK-GQGNTERTVWQYH
          S.VIVMT.KEVERGKSKCVKYWPDEYA.KEYG.M.VRNVKESA.HDY.LRELKLSK.G.GN.ER.VWQYH
Retrocopy SQVIVMTMKEVERGKSKCVKYWPDEYAVKEYGIMHVRNVKESATHDYKLRELKLSKIGKGNMERMVWQYH

Parental  FRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDID
          F.TW..HGVP.D..G.L.FL.EVH.KQ.SIMDAG.VVVHCSAGIG.TGTFIVIDILIDIIREKGVDC.ID
Retrocopy FWTWLYHGVPCDSKGMLHFLDEVHRKQDSIMDAGLVVVHCSAGIGQTGTFIVIDILIDIIREKGVDCEID

Parental  VPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSP
          VPKTIQMV.SQRS.MVQTEAQYRFIYMAVQH.IETLQRRIEEEQKSKRKGHE.TNIKYSL.DQTSGDQSP
Retrocopy VPKTIQMVQSQRSEMVQTEAQYRFIYMAVQHHIETLQRRIEEEQKSKRKGHECTNIKYSLVDQTSGDQSP

Parental  LPPCTPTPPCAEMREDSARVYENVGLMQQQKSFR
          L.P.TP.PPCAEMRE.SARVYENVGLMQQQK..R
Retrocopy LLPYTPMPPCAEMREESARVYENVGLMQQQKHLR

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	0.22 RPM	68.95 RPM
SRP007412_cerebellum	0.85 RPM	26.75 RPM
SRP007412_heart	0.12 RPM	25.26 RPM
SRP007412_kidney	0.03 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_2205 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2205 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2205 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2823

---

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,