RetrogeneDB ID: retro_pabe_438

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:122461584..122463361(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP459A162
• Ensembl ID: ENSPPYG00000015835
• Aliases: None
• Description: None

Sequence

>retro_pabe_438
ATGTCCAAGTCATTCCAGCAGTCATCTCTCAGTAGGGACTCACAGGGTCATGGGTGTGACCTGTTTGCGGCAGGCATAGG
CCTTCCTGCTGCTGTTACCCAGTCTTTAAGTATGCCAGCATCTCTTGGAAGGATGAACCAGAGTACTGCAGGCCTTGCTA
GTTTAATGAATCTTGGAACGAGTTCTTCATTGAATCAACAAGGAGCTCATAGTGCACGGTCTTCTGCTAGTACTTCTTCC
CATAATTTACAGTCTATATTTAACATTGGAAGTAGAGGTCCATGCCCTTTATCTTCTCAACACCGTAGCGATGCAGACCA
GGCCAGTAACATTTTGGCCAGCTTTGGTTTGTCTGCTGGAGACTTAGATGAACTGAGCCGTTATCCAGAGGACAAGATGC
CTCCTGAGAATTTGCCCCAAATCCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACCTTGAGTTATGGTAGA
GATGACAGATCTGCTGCATGGGAGCCACCATACAGAGTACCTAGGGATGATTGGGAAGAAAAAAAGTCACTTTAGAAGAG
ATAGTTTTGATGATCGTGGTCCTAGTCTCAACCTGGTGCTTGATTATGATCATGGAAGTCATTCTCAAGAATCTGGATAT
TATGACAGAATGGATTATGAAGATGACAGATTACGAGATGGAGAAAGGTGTAGGGATGAGTCTTTTTTCGGTGAGACCTC
GCATAACTATCATAAATTTGACAGTGAGTATGAGAGAATGGGACGTGTTCATGGTCCTGACCCCTTACAAGAGAGATCTC
TCTTTGAGAAAAAGAAGGGCGCTCCTCCAAGTAGCAATATTGAAGACTTTCATGGGCTCTTACTGAAAGGTTATACCCAT
CTGTGCTCTATATGTGATTTGCCGGTTCATTCTAATGAGGTGTTGAGTCAACATATCAATGGAGCAAGCCACAATCGTCG
ATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACAGAACACACAGTGGGCGATCCATTCATGT
TGCAGCATTCTACAAACCCAGCACCAGGAATTCTGGGATCTCCACCTCCCTCGTTTCATCTTGGAGGACCAGCAATTGGA
CCAAGAGGAAATCTGGGTCCTGGAAATGGAAATCTGCAAAGAACTAGACACATAAAAAATGGCAGAGTGGAAACTAGCAG
AGTTGTTCACATCATGGATTTTCAGCGAGGGAAAAACTTGAGATACCAGCTATTACAGCTGGTAGAACCATTTGGAGTCA
TTTCAAGTCATCTGCTTCTAAATAAAATTAATGAGGCATTTATTGAAAGGGCAACCACAGAGGATGCTCAGGCTGCAGTG
GATTATTATACAACCACAACAGCGTTAGTATTAGGCAAGCCAGTGAGAGTTCATTTAGCCCAGAAGTATAAAAGAATAAA
GAAGCCTGAAGGAAATCCAGATCAGAAGTTTGATCAAAGGCAAGAGCTCGGATGTATGATACATCTCAGCAATTTGCCCC
ATTCTGCCTATTCTGATAGTGCTGTTCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTACATATTGATGAGTATG
AAAAGTCAGGCTTTTATTGAGATGGAGACAAGAGAAGATGCAATGGCAATGGTTGACCATTGTTTGAAAAAAGCCCTTTA
GTTTCAGGAGAGATGTGTGAAGGCAGACCTGTCTGAGAAATATAAAAAACTGGTACTGAGGATTCCAAACAGAGGCATTG
ATTTACTGAAAAAAGAT

Alignment

ORF - retro_pabe_438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.39 %
• Parental protein coverage: 65.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKSFQQSSLSRDSQGHGRDLSAAGIGLLAAATQSLSMPASLGRMNQGTARLASLMNLGMSSSLNQQGAH
          MSKSFQQSSLSRDSQGHG.DL.AAGIGL.AA.TQSLSMPASLGRMNQ.TA.LASLMNLG.SSSLNQQGAH
Retrocopy MSKSFQQSSLSRDSQGHGCDLFAAGIGLPAAVTQSLSMPASLGRMNQSTAGLASLMNLGTSSSLNQQGAH

Parental  SALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDADQASNILASFGLSARDLDELSRYPEDKITPENLPQ
          SA.SSASTSSHNLQSIFNIGSRGP.PLSSQHR.DADQASNILASFGLSA.DLDELSRYPEDK..PENLPQ
Retrocopy SARSSASTSSHNLQSIFNIGSRGPCPLSSQHRSDADQASNILASFGLSAGDLDELSRYPEDKMPPENLPQ

Parental  ILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKR-HFRRDSFDDRGPSLNPVLDYDHGSRSQ
          ILLQLKRRRTEEGPTLSYGRD.RSA..EPPYRVPRDDWEEK..HFRRDSFDDRGPSLN.VLDYDHGS.SQ
Retrocopy ILLQLKRRRTEEGPTLSYGRDDRSAAWEPPYRVPRDDWEEKK>HFRRDSFDDRGPSLNLVLDYDHGSHSQ

Parental  ESGYYDRMDYEDDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGR--GPGPLQERSLFEKKRGAPPSSN
          ESGYYDRMDYEDDRLRDGERCRD.SFFGETSHNYHKFDSEYERMGR..GP.PLQERSLFEKK.GAPPSSN
Retrocopy ESGYYDRMDYEDDRLRDGERCRDESFFGETSHNYHKFDSEYERMGRVHGPDPLQERSLFEKKKGAPPSSN

Parental  IEDFHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQ
          IEDFHGLL.KGY.HLCSICDLPVHSN...SQHINGASH.RRCQLLLEIYPEWNPDNDT.HT.GDPFMLQ.
Retrocopy IEDFHGLLLKGYTHLCSICDLPVHSNEVLSQHINGASHNRRCQLLLEIYPEWNPDNDTEHTVGDPFMLQH

Parental  STNPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQ
          STNPAPGILG.PPPSFHLGGPA.GPRGNLG.GNGNLQ..RH...GRVETSRVVHIMDFQRGKNLRYQLLQ
Retrocopy STNPAPGILGSPPPSFHLGGPAIGPRGNLGPGNGNLQRTRHIKNGRVETSRVVHIMDFQRGKNLRYQLLQ

Parental  LVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQK
          LVEPFGVIS.HL.LNKINEAFIE.ATTEDAQAAVDYYTTT.ALV.GKPVRVHL.QKYKRIKKPEG.PDQK
Retrocopy LVEPFGVISSHLLLNKINEAFIERATTEDAQAAVDYYTTTTALVLGKPVRVHLAQKYKRIKKPEGNPDQK

Parental  FDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKAL
          FDQ.QELG..IHLSNLPHS.YSDSAVLKLAEPYGKIKNYILM.MKSQAFIEMETREDAMAMVDHCLKKAL
Retrocopy FDQRQELGCMIHLSNLPHSAYSDSAVLKLAEPYGKIKNYILMSMKSQAFIEMETREDAMAMVDHCLKKAL

Parental  WFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKD
          .FQ.RCVK.DLSEKYKKLVLRIPNRGIDLLKKD
Retrocopy *FQERCVKADLSEKYKKLVLRIPNRGIDLLKKD

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	0.00 RPM	296.36 RPM
SRP007412_cerebellum	0.00 RPM	493.94 RPM
SRP007412_heart	0.00 RPM	124.42 RPM
SRP007412_kidney	0.00 RPM	130.86 RPM
SRP007412_liver	0.00 RPM	88.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_438 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_438 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006888	1 retrocopy	retro_cjac_3950,
Homo sapiens	ENSG00000015479	1 retrocopy	retro_hsap_199,
Gorilla gorilla	ENSGGOG00000007308	2 retrocopies	retro_ggor_276, retro_ggor_421,
Nomascus leucogenys	ENSNLEG00000009093	1 retrocopy	retro_nleu_1849,
Oryctolagus cuniculus	ENSOCUG00000026311	1 retrocopy	retro_ocun_652,
Otolemur garnettii	ENSOGAG00000010607	1 retrocopy	retro_ogar_3417,
Pongo abelii	ENSPPYG00000015835	2 retrocopies	retro_pabe_1722, retro_pabe_438 ,
Pan troglodytes	ENSPTRG00000017294	1 retrocopy	retro_ptro_181,
Rattus norvegicus	ENSRNOG00000019875	2 retrocopies	retro_rnor_1124, retro_rnor_475,