RetrogeneDB ID: retro_pabe_3293

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:133811465..133812637(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KNOP1
• Ensembl ID: ENSPPYG00000007151
• Aliases: None
• Description: lysine-rich nucleolar protein 1 [Source:HGNC Symbol;Acc:34404]

Sequence

>retro_pabe_3293
AAGGGGGATGGGGAAGTTTGGCCCACCGGAATGACCACCAAGACATACAAAGTAGACCTGGGCCCTGGGCTCCCAGAGAA
GAAAAAGAAGAAGAAAGTGGTCAAAGAACCGGAGACTCAATACTCAATTTTAAACAATGATGATTACTTTGCCAATGTTT
CTCCTATAAGAGTCACATCCCCCTCTAAGACTGTAGTCCATGGACAGGCACCTGAGATGCCTCTAGTGAAGAAAAAGAAG
GAGAAAAAGAAGGGTGTCAGCACCCTTTGCAAGGAGCATGTAGAACCTGAGACCACGCTGTGTGCCAGATGGACAGAGAA
GTCACCCAGCCCCAGGAAGCAGGTGCTTGGCCACTTGAAGTTCCTCAGTGGGGAGAAGAAAAAGAAGTCACCTCAGGCTA
TGTCCCATGCCTCTGGGGTGAAAACCTCCCCAGACCTCAGACGTAGTGAGGAGGAAATCAGAGATGGAAAGAAACTCAAA
AAACACAAGAAGGCAAAAAATAGGGGTCCAGGACCCCACAGCCTTCTCAGTCCAGGACCCTTGGTTCTGCGAGGCCGGGA
TGCTGTGGACACTTGCTCAGTGGGGAAAGAGGGTGAGGAACAGGCAGCCTTGGGGCAGAAACAGAAGCAGAAGAGCCCCA
GGGAACACAGTGGGAAGGTGAAGAAGAAAAAAAAATTCCACCAGGAGGGAGACGTCCTCCCAGGCCACTCCAAGCCCTCC
AGGTCCTTGGAGAGCAGCCCCCGTAAAGGAAGTAAAACTAAACCAGTCGAAGTTGAGGCTCCAGAATATATCCTCATAGG
AGATGGCCCTAAGGCCCCCGCGAAGAAAAAGATGAAGTCCAAGAAGAAGGTCACTGAGGAGCCGGCTCTGAAAAGGAAGC
AAAAAATAAGAGGAAAGAGAGTGGAGTAGCAGGAGACCCTTGGAAGGAGGAAAAAGACACGGACTTAGAGGTGGTGTTGG
AAAGGAAAGGCAATATGGACGAGGCACACATAGACCAGGTGAGGCAAAAGGCCTTGCAAGAAGAGGTCCATTGCGAGTCA
GGCAAAACGGAAGCTTCTGAAACCTGGAAGTGGATGGGAACCCAGTTTGGCTAGTGGGATACTGCTGGTTTTGAGAACAA
GGAACAGAAACTGAAATTTCTCAAACTTATGGGTGGCTTCAAAAATCCGTCC

Alignment

ORF - retro_pabe_3293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.1 %
• Parental protein coverage: 77.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RGGGEISPTGMITKTHKVD--PGLPEKKKKKKVVKEPETRYSVLN-DDYFADISPVRATSPSKSVAHGQA
          .G.GE..PTGM.TKT.KVD..PGLPEKKKKKKVVKEPET.YS.LN.DDYFA..SP.R.TSPSK.V.HGQA
Retrocopy KGDGEVWPTGMTTKTYKVDLGPGLPEKKKKKKVVKEPETQYSILNNDDYFANVSPIRVTSPSKTVVHGQA

Parental  PEMPLVKKKKKKKKGVSTLCEEHVEPETTLPARRTEKSPSSRKQVLGHLEFLSGEKKKKKSPLAMSHASG
          PEMPLVKKKK.KKKGVSTLC.EHVEPETTL.AR.TEKSPS.RKQVLGHL.FLSGEKKKK.SP.AMSHASG
Retrocopy PEMPLVKKKKEKKKGVSTLCKEHVEPETTLCARWTEKSPSPRKQVLGHLKFLSGEKKKK-SPQAMSHASG

Parental  VKTSADPRQGEEETRVGKKLKKHKKEKK-GAQDPTAFSVQDPWFCEA-REARDVGDTCSVGKKDEEQAAL
          VKTS.D.R..EEE.R.GKKLKKHKK.K..G.QDPTAFSVQDPWFCEA.R.A.D...TCSVGK..EEQAAL
Retrocopy VKTSPDLRRSEEEIRDGKKLKKHKKAKN>GVQDPTAFSVQDPWFCEA<RDAVD---TCSVGKEGEEQAAL

Parental  GQKRKRKSPREHNGKVKKKKKIHQEGDALPGHSKTSRSMESSPRKGSKKKPVKVEAPEYIPISDDPKAST
          GQK.K.KSPREH.GKVKK....HQEGD.LPGHSK.SRS.ESSPRKGSK.KPV.VEAPEYI.I.D.PKA..
Retrocopy GQKQKQKSPREHSGKVKKXXXFHQEGDVLPGHSKPSRSLESSPRKGSKTKPVEVEAPEYILIGDGPKAPA

Parental  KKKMKSKKKVEQPVIEEPALKRKK-KKKRKESGVAGDPWKEETDTDLEVVLEKKGNMDEAHIDQVRRKAL
          KKKMKSKKKV......EPALKRK..K.KRKESGVAGDPWKEE.DTDLEVVLE.KGNMDEAHIDQVR.KAL
Retrocopy KKKMKSKKKVTE----EPALKRKQ<KNKRKESGVAGDPWKEEKDTDLEVVLERKGNMDEAHIDQVRQKAL

Parental  QEEIDRESGKTEASETRKWTGTHFQ-WDTAGFENEDQKLKFLRLMGGFKNLS
          QEE...ESGKTEASET.KW.GT.F..WDTAGFEN..QKLKFL.LMGGFKN.S
Retrocopy QEEVHCESGKTEASETWKWMGTQFG*WDTAGFENKEQKLKFLKLMGGFKNPS

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	4.92 RPM
SRP007412_cerebellum	0.00 RPM	8.76 RPM
SRP007412_heart	0.00 RPM	3.16 RPM
SRP007412_kidney	0.00 RPM	6.86 RPM
SRP007412_liver	0.03 RPM	6.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3293 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3293 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3293 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4007
Gorilla gorilla	retro_ggor_2691

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018032	2 retrocopies	retro_cfam_1557, retro_cfam_1763,
Callithrix jacchus	ENSCJAG00000009625	1 retrocopy	retro_cjac_3199,
Homo sapiens	ENSG00000103550	3 retrocopies	retro_hsap_3487, retro_hsap_4007, retro_hsap_979,
Gorilla gorilla	ENSGGOG00000005673	1 retrocopy	retro_ggor_2691,
Macaca mulatta	ENSMMUG00000002707	2 retrocopies	retro_mmul_1771, retro_mmul_798,
Nomascus leucogenys	ENSNLEG00000012496	2 retrocopies	retro_nleu_1618, retro_nleu_551,
Otolemur garnettii	ENSOGAG00000010065	4 retrocopies	retro_ogar_1115, retro_ogar_1480, retro_ogar_1481, retro_ogar_2259,
Pongo abelii	ENSPPYG00000007151	3 retrocopies	retro_pabe_3293 , retro_pabe_828, retro_pabe_920,
Pan troglodytes	ENSPTRG00000007836	3 retrocopies	retro_ptro_2360, retro_ptro_767, retro_ptro_924,