RetrogeneDB ID: retro_mmul_798

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:24845651..24846386(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000001025
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_798
CACCAGGAGGGAGACGCCCTCCCAGGCCACTCCAAGCCCTCCAGGTCCATGGAGAGCTGCCCTAGGAAACGAAGTAAAAA
GAAACCAGTCAAAGCGGAGGCTCCGGAATACATCCCCATAGGAGATGGCCCTAAGGCTCCTGCGAAGAAAAAGATGAAGT
CCAAGAAGAAGGTAGAGCGTCAGTCATTGAGGAGCCGGCTCTGAAAAGGAAGAAAAAGAAGAAGAGAAAAGAATGGGGTA
GCAGGAGAACCTTGGGAGGAGGAAACAGACACGGACTTAGAAGTGGTGTTGGAAAAGAAAGGCAACATGGACGAGGCGCA
CATAGACCAGGTGAGACGAAACACCTTGCAAGAAGAGATTGATCGCGAGTCAGGCAAAACGGAAGCTTCTGAAACCAGGG
AGTGGACGGGAACCCAGTTTGGCCAGTGGGATACCGCTGGTTTTGAAAACGAGGAACAGAAACTGAAATTTCTCAAACTT
TTGGGTGGCTTCAAAAACCTGTCCCCTTCGATTAGCCCCCACCCCCACCCTCCGGCCCCATCCAGCCCGATTGCAAGGTC
CAACATAGCCCTCAGCAAAAAGGTGGCCGACAGCCTGCAGCAGAGCCTGCAGCGGGACTACGACCTGGCCATGAGCTGGA
AGCACAGCCGCGCAGCCGGCCTCAGCTTCTCCACCATCCCCAACAAGATGTTTTATACTGACAGGAACGCTTCCAAGTCA
GTCAAGCCGGAAGAT

Alignment

ORF - retro_mmul_798 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.11 %
• Parental protein coverage: 52.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HQEEDTLPGHSKPSRSMESSPRKGSKKKPVKAEAPEYIPRSDDPKASAKKKMKSKKKVEQPVIEEPALKR
          HQE.D.LPGHSKPSRSMES.PRK.SKKKPVKAEAPEYIP..D.PKA.AKKKMKSKKKVE...........
Retrocopy HQEGDALPGHSKPSRSMESCPRKRSKKKPVKAEAPEYIPIGDGPKAPAKKKMKSKKKVERQSLRSRLXXX

Parental  KKKKRKESGVAGDPWKEETDTDLEVVLEKKGNMDEAHIDQVRRKALQEEIDRESGKTEASETRKWTGTQF
          ........GVAG.PW.EETDTDLEVVLEKKGNMDEAHIDQVRR..LQEEIDRESGKTEASETR.WTGTQF
Retrocopy XXXXXXXXGVAGEPWEEETDTDLEVVLEKKGNMDEAHIDQVRRNTLQEEIDRESGKTEASETREWTGTQF

Parental  GQWDTAGFENEDQKLKFLRLMGGFKNLSPP----PSNRAPST-TARPNMALSKKAADSLQQNLQRDYDRA
          GQWDTAGFENE.QKLKFL.L.GGFKNLSP.....P...APS...AR.N.ALSKK.ADSLQQ.LQRDYD.A
Retrocopy GQWDTAGFENEEQKLKFLKLLGGFKNLSPSISPHPHPPAPSSPIARSNIALSKKVADSLQQSLQRDYDLA

Parental  MSWKYSHSRGAGLGFSTAPNKIFYIDRNASKSVKLED
          MSWK..HSR.AGL.FST.PNK.FY.DRNASKSVK.ED
Retrocopy MSWK--HSRAAGLSFSTIPNKMFYTDRNASKSVKPED

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	0.34 RPM	68.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_798 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_798 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_798 has 0 orthologous retrocopies within eutheria group .

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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,