RetrogeneDB ID: retro_pabe_920

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:45400057..45401152(-)
• Located in intron of: ENSPPYG00000004433

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_920
AAGGAGCACCTAGAACCTGAGGCCATGTCGTGTGACAGACGGACAGGGAAGTCACCCAGCCCCAGGAAGCAGGCGCTTGG
CCACTTGGAGTTCCTCAGCGGGGACAAGAAAAAGAAGTGACCTCTGGCATGTTCCACGGTTCTGGGGTGAAAACCTCCCC
AGATCTCAGACAGAGTGAGGAGGAGACCAGAGTTGGCAAGAAGTTCAAAAAACACAAGAGGGGAAAAAAGAGGCCCAGGA
CCCCAGAGCCTTCTCAGTCCAGGACCCTTGATTCTGCAAGGAAAAGAATGTTGCCTACATTTGCTCAGTGGGGAAGGAGG
GCAAGGAGCAGGCAGCCTTGGGGCAGAACGGAAGCAGGGGAGGCCCAGGGAACACAGTGGTTAAGTGAAGAAGACAAAAA
AATCCACCAGAAGGGAGACACCCTCCTAGGCCACACCCCAAGCCCTCCAGGTCCATGAAGTGTAGCCTTAGGATACGAAG
TAAAAAGAAGCCAGTCAAAATTGAGGCTCCAAAATACATCGCAATATGCAATGGCCCTAAGGTCACAGCAAAGAAGAAAC
TGAAGTCCAAGAAAAACAGATCAGCCACTCACTGAGGACGTGGCTCTGAAAAGGAAAAAAAGAAGAGGAAAGAGAGCGGG
GTAGCAGGAAACTCATAGAAAGAGAGAACAGACAGACACAGAGGTTATGTTGGAAAAGAAAGGCAACATGGACAAGGGGC
ACAGAGACCAGGTGAGGTGGAAGGCCTTGCAACAGACTGATCTTTAGCTGGGCAAAAGAGAAGCTTCTGAAACCAGGAAG
TGGACAGTAACCCAGTTTGGCCAGTGGGATACTGGTTTTAAGAACAAGGAACAGAAATGGAAATTTCTCAAACATGGGTG
GATTCAAAAATCTGACCCCTTCATTCAGCTGCCCCCCTAGCATGACTGCAAGGCCCAACATGACCCTCAGCAAGAAGGCA
GCAAATAGCTTGCAGCAGAACCTGCAGCAGGACTACAACTAGGCCATGAGCTGGAAGTTCAACCTAGGAGCAGGCTTTGG
CTTCTCCAATGCCTCAAACAAAATCTTTTATATTGGCAGGAATGCTTCCAAGTCA

Alignment

ORF - retro_pabe_920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.62 %
• Parental protein coverage: 73.77 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  EEHVEPETTLPARRTEKSPSSRKQVLGHLEFLSGEKKKKKSPLAMS-HASGVKTSADPRQGEEETRVGKK
          .EH.EPE.....RRT.KSPS.RKQ.LGHLEFLSG.KKKK..PLA.S.H.SGVKTS.D.RQ.EEETRVGKK
Retrocopy KEHLEPEAMSCDRRTGKSPSPRKQALGHLEFLSGDKKKK*-PLACS<HGSGVKTSPDLRQSEEETRVGKK

Parental  LKKHKKEKKG-AQDPTAFSVQDPWFCEAREARDVGDTCSVGKKDEEQAALGQ-KRKRKSPREHNGKVKKK
          .KKHK..KK..AQDP.AFSVQDP.FC.......V...CSVGK...EQAALGQ..RK...PREH.G.VKK.
Retrocopy FKKHKRGKKR<AQDPRAFSVQDP*FCKEK---NVAYICSVGKEGKEQAALGQ<ERKQGRPREHSG*VKKT

Parental  KK-IHQ-EGDALPG-HSKTSRSMESSPRKGSKKKPVKVEAPEYIPISDDPKASTKKKMKSKKK-VEQPVI
          KK.IHQ.EG...P..H.K.SRSM..S.R..SKKKPVK.EAP.YI.I...PK..T.KK....KK...QP..
Retrocopy KK<IHQ<EGRHPPRPHPKPSRSMKCSLRIRSKKKPVKIEAPKYIAICNGPKV-TAKKKLKSKK>TDQPLT

Parental  EEPALKRKKKKKRKESGVAGDPWKEETDTDLEVVLEKKGNMDEAHIDQVRRKALQEEIDRESGKTEASET
          E..ALKRKK...............E.TDT..EV.LEKKGNMD..H.DQVR.KALQ...D...GK.EASET
Retrocopy EDVALKRKKRRGKRAG*QETHRKREQTDT--EVMLEKKGNMDKGHRDQVRWKALQ-QTDL*LGKREASET

Parental  RKWTGTHF-QWDTAGFENEDQKLKFLRLMGGFKNLSP-SFSRPAGTIARPNMALGKKAADSLQQNLQRDY
          RKWT.T.F.QWDT.GF.N..QK.KFL...G......P.SFS.P....ARPNM.L.KKAA.SLQQNLQ.DY
Retrocopy RKWTVTQFGQWDT-GFKNKEQKWKFLK-HGWIQKSDP>SFSCPPSMTARPNMTLSKKAANSLQQNLQQDY

Parental  DRAMSWKYSRGAGLGFSTAPNKIFYIDRNASKS
          ..AMSWK...GAG.GFS.A.NKIFYI.RNASKS
Retrocopy N*AMSWKFNLGAGFGFSNASNKIFYIGRNASKS

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	4.92 RPM
SRP007412_cerebellum	0.36 RPM	8.76 RPM
SRP007412_heart	0.09 RPM	3.16 RPM
SRP007412_kidney	0.23 RPM	6.86 RPM
SRP007412_liver	0.18 RPM	6.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_920 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_920 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_920 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_3199

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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,