RetrogeneDB ID: retro_mmul_1771

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:69227101..69227877(+)
• Located in intron of: ENSMMUG00000015320

Retrocopy information

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

Parental gene information

• Parental gene symbol: KNOP1
• Ensembl ID: ENSMMUG00000002707
• Aliases: None
• Description: lysine-rich nucleolar protein 1 [Source:HGNC Symbol;Acc:34404]

Sequence

>retro_mmul_1771
CACAAGAAGGAAACAAAGGGGGCCCAGGACCCCTCAGTCCAGGATCCTTGATTCTGCAAGGCTGGTGATGCTGCCAACAC
CTGCTCAGTGGGGAAGAAGGGTGAGGAACAGGCAACCTTGGGGCAGATAAGGGAAGCAGAAGAGCCCCAGGGAACACAGT
GGGAAGGTGAAGAAGAAGAAAAAAAAATCCACCAGGAGGGAGACGCCCTCCCAGGCCACTCCAAGCCTTCCAGGTCCATG
GAGAGCAGCCCTAGGAAAGGAAGTAAAAAGAAGCCAAAGTTGAGGATCCGGAATACATCCACCCCCATAGGAAATGGCCC
TAAGGCCCCCGCAAAGAAAACGATGAAGTCCAAGAAGGTAGAGCAGCCAATCATTGAGGAGCCAGCTCTGAAAAGGAAGA
AAAAGAAGAAGAGGAAAGAGAGTGGAGTAGCAAGAGATCCTTGGAAGGAGGAAACAGACACGGACTTAGAGGTGGTGTTG
GAAAAGAAAGGCAACATGGACGAGGCGCACATAGACCAGGTGAGGCGAAAGGCCTTGCAAGGAGAGATCCATCGCGAGTC
AGGCAAAATGGAAGCTTCTGAAACCAGGAAGTGGAGGGGAACCCAGTTTGGCCAGTGGGATACTGCTGATTTTGAGAACG
AGGAACAGAAACTGAAGTTTCTCAAACTTACGGGTGGCTTCAAAAACCTGTCCCCTTCGTTCAGCCGCCACCCCTCTCCA
CACTCCCCAGCACGATTGCAAGGCCCAACATGGCCCTCAGCAAGAAGGCGGCCGAC

Alignment

ORF - retro_mmul_1771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.75 %
• Parental protein coverage: 56.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HKKEKKGARDATAFSVQDPWFCEAREARDVADTCSVGKKDEGQAA-LG-QKRKRKSPREHNGKVKKKKKI
          HKKE.KGA.D....SVQDP.FC....A.D.A.TCSVGKK.E.QA..LG..K..R..P....G........
Retrocopy HKKETKGAQDP---SVQDP*FCK---AGDAANTCSVGKKGEEQAT<LGADKGSRRAPGNTVGR*RRXXXX

Parental  -HQEEDTLPGHSKPSRSMESSPRKGSKKKPVKAEAPEYIPRSDDPKASAKKKMKSKKKVEQPVIEEPALK
          .HQE.D.LPGHSKPSRSMESSPRKGSKKKP.........P....PKA.AKK.MKSKK.VEQP.IEEPALK
Retrocopy >HQEGDALPGHSKPSRSMESSPRKGSKKKPKLRIRNTSTPIGNGPKAPAKKTMKSKK-VEQPIIEEPALK

Parental  RKKKK-RKESGVAGDPWKEETDTDLEVVLEKKGNMDEAHIDQVRRKALQEEIDRESGKTEASETRKWTGT
          RKKKK.RKESGVA.DPWKEETDTDLEVVLEKKGNMDEAHIDQVRRKALQ.EI.RESGK.EASETRKW.GT
Retrocopy RKKKKKRKESGVARDPWKEETDTDLEVVLEKKGNMDEAHIDQVRRKALQGEIHRESGKMEASETRKWRGT

Parental  QFGQWDTAGFENEDQKLKFLRLMGGFKNLSPP----PSNRAP-STTARPNMALSKKAAD
          QFGQWDTA.FENE.QKLKFL.L.GGFKNLSP.....PS...P.ST.ARPNMALSKKAAD
Retrocopy QFGQWDTADFENEEQKLKFLKLTGGFKNLSPSFSRHPSPHSP<STIARPNMALSKKAAD

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	0.00 RPM	7.96 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.14 RPM
SRP007412_cerebellum	0.00 RPM	9.43 RPM
SRP007412_heart	0.00 RPM	7.95 RPM
SRP007412_kidney	0.00 RPM	11.62 RPM
SRP007412_liver	0.00 RPM	4.67 RPM
SRP007412_testis	0.00 RPM	68.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1771 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1771 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3487
Pan troglodytes	retro_ptro_2360

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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,