RetrogeneDB ID: retro_nleu_860

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:17801905..17802658(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKR1D1
• Ensembl ID: ENSNLEG00000013710
• Aliases: None
• Description: None

Sequence

>retro_nleu_860
TCTTCATCAGTGAAGGTTGTCATTGACCTGGGATGATGACACACTGATGAAGCCTACATATGCCAAAATGAAGACATAGC
TGGGGAGGCCATCAGGGGGTAAATAGCAGAAGGAAAGGTGCAGAGGAAGGATATCTACTGTGGAAAACTGTGGGCTACAA
ATCACGACCCAGAGCTGGTCTGCCCAAGTCTAGAGAGGATGCTCAATGTCCTCCAGCTAGATTGTGTGGCTCTTACATCA
CTGAAATACCCATGGCCCCTAAGCCTGAAGATGAAATCTACCCTATAGGTGAGAATGGCAAATTGTTATATCACAAGTCA
AATCTGTGTGCCACTTGGGAGACTTCGGAAGCTTGCAAAGATGCTGGCTTGGTGAAATCCCTCGGAGTATCCAGTTTTAA
CAGCAGGCCAGCTGGAGCTCATCCAGAACAACCCAGGACTCAAACCCAAGCCAGTCAGCAATGAGGTTGAGTGCCACCCA
TATTACACCCAGCCAAAACTTTTGAAATTTTGCCAACAACGTGACATTGTCATGATTGCATATAGCCCTTTGGGGACCAC
TGGGAATCCAACCTGGACAAATATGTCTTCTCCACCTTCGTTAAAGGATGCACTTCTAAAAAGGTGCAATAAGATCACAG
CTCAAGTTATTTTGCGTTTCAACATCCAGCAAGGGGTGGCTGTCATTCCTGAAAGCTTTAATCCTGAAAAGATCAAGGAA
AACCTTCAGGTCTTTGACTTTTCTCTCACCGAA

Alignment

ORF - retro_nleu_860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.03 %
• Parental protein coverage: 78.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATSVKVAIDTGYRHIDGAYIYQNEHEVGEAIREKIAEGKVRREDIFYCGKLWATNHVPDMVRPTLERTLR
          ..SVKV.ID.G..H.D.AYI.QNE...GEAIR..IAEGKV.R.DI.YCGKLWATNH.P..V.P.LER.L.
Retrocopy SSSVKVVIDLG**HTDEAYICQNEDIAGEAIRG*IAEGKVQRKDI-YCGKLWATNHDPELVCPSLERMLN

Parental  VLQLDYVDL-YIIEVPMAFKPGDEIYPRDENGKWLYHKSNLCATWEAMEACKDAGLVKSLGVSNFNRR-Q
          VLQLD.V.L.YI.E.PMA.KP.DEIYP..ENGK.LYHKSNLCATWE..EACKDAGLVKSLGVS.FN.R.Q
Retrocopy VLQLDCVAL<YITEIPMAPKPEDEIYPIGENGKLLYHKSNLCATWETSEACKDAGLVKSLGVSSFNSR>Q

Parental  LELILNKPGLKHKPVSNQVECHPYFTQPKLLKFCQQHDIVIIAYSPLGTSRNPTWVNISSPPLLKDALLN
          LELI.N.PGLK.KPVSN.VECHPY.TQPKLLKFCQQ.DIV.IAYSPLGT..NPTW.N.SSPP.LKDALL.
Retrocopy LELIQNNPGLKPKPVSNEVECHPYYTQPKLLKFCQQRDIVMIAYSPLGTTGNPTWTNMSSPPSLKDALL-

Parental  SLGKRYNKTAAQIVLRFNIQRGVVVIPKSFNLERIKENFQIFDFSLTE
          ...KR.NK..AQ..LRFNIQ.GV.VIP.SFN.E.IKEN.Q.FDFSLTE
Retrocopy ---KRCNKITAQVILRFNIQQGVAVIPESFNPEKIKENLQVFDFSLTE

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_860 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012872	1 retrocopy	retro_cjac_1688,
Homo sapiens	ENSG00000122787	1 retrocopy	retro_hsap_257,
Gorilla gorilla	ENSGGOG00000014684	1 retrocopy	retro_ggor_307,
Nomascus leucogenys	ENSNLEG00000013037	7 retrocopies	retro_nleu_1246, retro_nleu_1533, retro_nleu_2099, retro_nleu_2569, retro_nleu_2570, retro_nleu_418, retro_nleu_419,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Nomascus leucogenys	ENSNLEG00000013710	1 retrocopy	retro_nleu_860 ,
Pongo abelii	ENSPPYG00000018037	1 retrocopy	retro_pabe_406,
Pan troglodytes	ENSPTRG00000019740	1 retrocopy	retro_ptro_217,
Rattus norvegicus	ENSRNOG00000013004	1 retrocopy	retro_rnor_2559,