RetrogeneDB ID: retro_pabe_1722

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:21235933..21237384(+)
• 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_1722
AGTAACATTTTGGCCAGCTTTGGTTTGTCTGCTGGAGACTTAGATGAACTGAGCCGTTATCCAGAGGACAAGATGACTCC
TGAGAATTTGCCCCAAATCCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACCTTGAGTTATGGTAGAGATG
ACAGATCTGCTGCATGGGAGCCACCATACAGAGTACCTAGGGATGATTGGGAAGAAAAAAAGTCACTTTAGAAGAGATAG
TTTTGATGATCGTGGTCCTAGTCTCAACCTGGTGCTTGATTATGATCATGGAAGTCATTCTCAAGAATCTGGATATTATG
ACAGAATGGATTATGAAGATGACAGATTACGAGATGGAGAAAGGTGTAGGGATGAGTCTTTTTTTGGTGAGACCTCGCAT
AACTATCATAAATTTGACAGTGAGTATGAGAGAATGGGACGTGTTCATGGTCCTGACCCCTTACAAGAGAGATCTCTCTT
TGAGAAAAAGAAGGGCGCTCCTCCAAGTAGCAATATTGAAGACTTTCATGGACTCTTACTGAAAGGTTATACCCATCTGT
GCTCTATATGTGATTTGCCAGTTCATTCTAATGAGGTGTTGAGTCAACATATCAATGGAGCAAGCCACAATCGTCGATGC
CAGCTTCTTCTTGAAATCTACCCAGAATGGAATCCTGACAATGATACAGAACACACAGTGGGCGATCCATTCATGTTGCA
GCATTCTACAAACCCAGCACCAGGAATTCTGGGATCTCCACCTCCCTCGTTTCATCTTGGAGGACCAGCAATTGGACCAA
GAGGAAATCTGGGTGCTGGAAATGGAAATCTGCAAAGAACTAGACACATAAAAAATGGCAGAGTGGAAACTAGCAGAGTT
GTTCACATCATGGATTTTCAGCGAGGGAAAAACTTGAGATACCAGCTATTACAGCTGGTAGAACCATTTGGAGTCATTTC
AAGTCATCTGATTCTAAATAAAATTAATGAGGCATTATTGAAAGGGCAACCACAGAGGATGCTCAGGCTGCAGTGGATTA
TTATACAACTACAACAGTGTTAGTATTAGCAAGCCAGTGAGAGCTCATTTAGCCCAGAAGTATAAAAGAATAAAGAAACC
TGAAGGAAAGCCAGATCAGAAGTTTGATCAAAGGCAAGAGCTCGGATGTATGATACATCTCAGCAATTTGCCCCATTCTG
CCTATTCTGATAGTGCTGTTCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTACATATTGATGAGTATGAAAAGT
CAGGCTTTTATTGAGATGGAGACAAGAGAAGATGCAATGGCAATGGTTGACCATTGTTTGAAAAAAGCCCTTTAGTTTCA
GGAGAGATGTGTGAAGGCAGACCTGTCTGAGAAATATAAAAAACTGGTACTGAGGATTCCAAACAGAGGCATTGATTTAC
TGAAAAAAGAT

Alignment

ORF - retro_pabe_1722 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.94 %
• Parental protein coverage: 53.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SNILASFGLSARDLDELSRYPEDKITPENLPQILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDW
          SNILASFGLSA.DLDELSRYPEDK.TPENLPQILLQLKRRRTEEGPTLSYGRD.RSA..EPPYRVPRDDW
Retrocopy SNILASFGLSAGDLDELSRYPEDKMTPENLPQILLQLKRRRTEEGPTLSYGRDDRSAAWEPPYRVPRDDW

Parental  EEKR-HFRRDSFDDRGPSLNPVLDYDHGSRSQESGYYDRMDYEDDRLRDGERCRDDSFFGETSHNYHKFD
          EEK..HFRRDSFDDRGPSLN.VLDYDHGS.SQESGYYDRMDYEDDRLRDGERCRD.SFFGETSHNYHKFD
Retrocopy EEKK>HFRRDSFDDRGPSLNLVLDYDHGSHSQESGYYDRMDYEDDRLRDGERCRDESFFGETSHNYHKFD

Parental  SEYERMGR--GPGPLQERSLFEKKRGAPPSSNIEDFHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASH
          SEYERMGR..GP.PLQERSLFEKK.GAPPSSNIEDFHGLL.KGY.HLCSICDLPVHSN...SQHINGASH
Retrocopy SEYERMGRVHGPDPLQERSLFEKKKGAPPSSNIEDFHGLLLKGYTHLCSICDLPVHSNEVLSQHINGASH

Parental  SRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTNPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQG
          .RRCQLLLEIYPEWNPDNDT.HT.GDPFMLQ.STNPAPGILG.PPPSFHLGGPA.GPRGNLGAGNGNLQ.
Retrocopy NRRCQLLLEIYPEWNPDNDTEHTVGDPFMLQHSTNPAPGILGSPPPSFHLGGPAIGPRGNLGAGNGNLQR

Parental  PRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEA-FIEMATTEDAQAAVDYY
          .RH...GRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVIS.HLILNKINEA..IE.ATTEDAQAAVDYY
Retrocopy TRHIKNGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISSHLILNKINEA<IIERATTEDAQAAVDYY

Parental  TTTPALV-FGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKI
          TTT..LV...KPVR.HL.QKYKRIKKPEGKPDQKFDQ.QELG..IHLSNLPHS.YSDSAVLKLAEPYGKI
Retrocopy TTTTVLV<ISKPVRAHLAQKYKRIKKPEGKPDQKFDQRQELGCMIHLSNLPHSAYSDSAVLKLAEPYGKI

Parental  KNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKD
          KNYILM.MKSQAFIEMETREDAMAMVDHCLKKAL.FQ.RCVK.DLSEKYKKLVLRIPNRGIDLLKKD
Retrocopy KNYILMSMKSQAFIEMETREDAMAMVDHCLKKAL*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_1722 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1722 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,