RetrogeneDB ID: retro_nleu_551

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:40344114..40345287(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16ORF88
• Ensembl ID: ENSNLEG00000012496
• Aliases: None
• Description: None

Sequence

>retro_nleu_551
AAGGGGGATGGGGAAGTTTGGCCCACCGGAATGATCACCAAGACACACAAAGTAGACCTGGGCCCTGGGCTCCCAGAGAA
GAAAAAGAAGAAGAAAGTGGTCAAAGAACCAGAGACTCAATACTCAGTTTTAAACAATGATGATTACTTTGCCGATGTTT
CTTCTATAAGAGCCACATCCCCCTCTAAGAGTGTAGTACATGGGCAGGCACCTGAGATGCCTCTAGTGAAGAAAAAGAAG
GAGAAAAAGAAGGGTGTCAGTGCCCTTTGCCAGGAGCATGTAGAACCTGAGACCACGCTGTGTGCCAGATGGACAGAGAA
GTCACGCAGCCCTAGGAAGCAGGTGCATGGCCACTTGAAGTTCCTCAGTGGGGAGAAGAAAAAGAAGTCACCTCAGGCTA
TGTCCCATGCCTCTGGGGTGAAAACCTCCCCAGACCTCAGACACAGTGAGGAGGAAACCAGAGTTGGAAAGAAACTCAAA
AAACACAAGAAGGCAAAAAATAGGGGGCCCAGGACCCCACAGCCTTCTCAGTCCAGGACCCTTGGTTCTGCGAGCCTGGG
ATGCTGCGGACACTGGCTCAGTGGGGAAGGAGGGGGAGGAACAGGCAGCCCTGGGGCAGAAACAGAAGCAGAAGAGCCCC
AGGGAACACAGTGGGAAGGTGAAGAAGAAAAAAAAAATTCCACCAGGAGGGAGACGTCCTCCCAGGCCACTCCAAGCCCT
CCAGGTCCTTGGAGAGCAGCCCCTGTAAAGGAAGTAAAACTAAACCAGTCAAAGTTGAGGCTCCAGAATATATCCCTATA
GGAGATGGCCCTAAGGCCCCCTCGAAGAAAAAGACGAAGTCCAAGAAGAAGGTCACTGAGGAGCCGGCTCTGAAAAGGAG
GAAAAAATAAGAGGAAAGAGAGTGGGGTAGCAGGAGACCCTTGGAAGGAGGAAACAGACACGGACTTAGAGGTGGCGTTG
GAAAAGAAAGGCAATATGGACCAGGCGCACATAGACCAGGTGAGGGGAAAGGCCTTTCAAGAAGAGGTCTATCGCGAGTC
AGGCAAAACGGAAGCTTCTGAAACCTGGAAGTGGACGGGAACCCAGTTTGGCCAGTGGGATACTGCTGGTTTTCAGAACG
AGGAACAGAAACTGAAATTTCTCAAACTTATGGGTGGCTTCAAAAATCTGTCC

Alignment

ORF - retro_nleu_551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.47 %
• Parental protein coverage: 76.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RGGGEISPTGMITKTHKVD--PGLPEKKKKKKVVKEPETRYSVLNNDDYFADVSPIRATSPSKSVAHGQA
          .G.GE..PTGMITKTHKVD..PGLPEKKKKKKVVKEPET.YSVLNNDDYFADVS.IRATSPSKSV.HGQA
Retrocopy KGDGEVWPTGMITKTHKVDLGPGLPEKKKKKKVVKEPETQYSVLNNDDYFADVSSIRATSPSKSVVHGQA

Parental  PEMPLVKKKKKKKKGVSTLCKKHVEPETTLPARWTEKSPSPRKQVLGHLEFLSGEKKRKKSPLAMSHASG
          PEMPLVKKKK.KKKGVS.LC..HVEPETTL.ARWTEKS.SPRKQV.GHL.FLSGEKK.KKSP.AMSHASG
Retrocopy PEMPLVKKKKEKKKGVSALCQEHVEPETTLCARWTEKSRSPRKQVHGHLKFLSGEKK-KKSPQAMSHASG

Parental  VKTSPDPRQGEEETRVGKKLKKH-KKEKK-GAQDPTAFLVQD-PWVCEAREARDVGDSCSVGKKDEKQAA
          VKTSPD.R..EEETRVGKKLKKH....KK.GAQDPTAF.VQD.P.V..A..A.D.G...SVGK..E.QAA
Retrocopy VKTSPDLRHSEEETRVGKKLKKH<QEGKK*GAQDPTAFSVQD<PLVLRAWDAADTG---SVGKEGEEQAA

Parental  LGQK-RKQKSPREYNGKVKKKK-IHQEGDVLPGHSKPSRSMESSPRKGSKKKPVKVEAPEYIPVSDDPKA
          LGQK.R....P....G........HQEGDVLPGHSKPSRS.ESSP.KGSK.KPVKVEAPEYIP..D.PKA
Retrocopy LGQK>RSRRAPGNTVGR*RXXXXFHQEGDVLPGHSKPSRSLESSPCKGSKTKPVKVEAPEYIPIGDGPKA

Parental  SAKKKMKSKKKVEQPVIEEPALKRKKKK-KRKESGVAGDPWKEETDTDLEVVLEKKGNMDEAHIDQVRRK
          ..KKK.KSKKK....V.EEPALK...KK.KRKESGVAGDPWKEETDTDLEV.LEKKGNMD.AHIDQVR.K
Retrocopy PSKKKTKSKKK----VTEEPALK-RRKK>KRKESGVAGDPWKEETDTDLEVALEKKGNMDQAHIDQVRGK

Parental  ALQEEIDRESGKTEASETRKWTGTQFGQWDTAGFENEDQKLKFLRLMGGFKNLS
          A.QEE..RESGKTEASET.KWTGTQFGQWDTAGF.NE.QKLKFL.LMGGFKNLS
Retrocopy AFQEEVYRESGKTEASETWKWTGTQFGQWDTAGFQNEEQKLKFLKLMGGFKNLS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_551 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,