RetrogeneDB ID: retro_nleu_198

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:70088810..70089288(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM173B
• Ensembl ID: ENSNLEG00000011587
• Aliases: None
• Description: family with sequence similarity 173, member B [Source:HGNC Symbol;Acc:27029]

Sequence

>retro_nleu_198
GGTACATCCCTAGAAACACTTAAAGAAGAAAGTCAGTCAAGACATATTCTACCTTTGACTTTTGAAGCCAACCGTTTGAA
GAAAAGCAACTAGGGGTTTTTATTTATTGAGATTGTGGGTGGGGCTCTGGTGGCTGTATGCTGTAGCTATGCCATTTATA
GCACCAATCCTCTCAAAAGTCTGTTTGCCTTTTGTACCTGCAACTACAAAGCAGATCAAAAATGTGAAAATGTTGCTATG
CAGAGGAGGATCCCTGGTAGACATTGGTAATGGCAATGGACACATTAATAACACAGTAATAGCAGCTGCAAAGGAAAGAT
TCACGGCAGTTGGTTGTGAATTTAATCCGTGGCTAGTTTGGTATTCCAAGTATCATGCTTGGCAAGAAAGTGTGCATGGC
TCTGCCAAATTTTATATTTCAGATTTGTGGGCAGTTACTTTTTCATAGTACTCAAACACTGTTATTTTTGGTGTGCCT

Alignment

ORF - retro_nleu_198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.46 %
• Parental protein coverage: 57.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GIPLETLKEESQSRHALPASFEANSLLKSN-WGFLLTGLVGGTLVAVYAVATPFVTPALRKVCLPFVPAT
          G..LETLKEESQSRH.LP..FEAN.L.KSN..GF.L..L..G.L...YAVA.PF..P.L.KVCLPFVPAT
Retrocopy GTSLETLKEESQSRHILPLTFEANRLKKSN>RGFYLLRLWVG-LWWLYAVAMPFIAPILSKVCLPFVPAT

Parental  TKQIENVVKMLRCRRGSLVDIGSGDGRI---VIAAAKEGFTAVGYELNPWLVWYSRYRAWREGVHGSAKF
          TKQI.NV.KML.CR.GSLVDIG.G.G.I...VIAAAKE.FTAVG.E.NPWLVWYS.Y.AW.E.VHGSAKF
Retrocopy TKQIKNV-KMLLCRGGSLVDIGNGNGHINNTVIAAAKERFTAVGCEFNPWLVWYSKYHAWQESVHGSAKF

Parental  YISDLWKVTFSQYSNVVIFGVP
          YISDLW.VTFS.YSN.VIFGVP
Retrocopy YISDLWAVTFS*YSNTVIFGVP

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_198 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002277	1 retrocopy	retro_dnov_1076,
Homo sapiens	ENSG00000150756	1 retrocopy	retro_hsap_1105,
Macaca mulatta	ENSMMUG00000020111	1 retrocopy	retro_mmul_858,
Nomascus leucogenys	ENSNLEG00000011587	1 retrocopy	retro_nleu_198 ,
Oryctolagus cuniculus	ENSOCUG00000025588	1 retrocopy	retro_ocun_1244,
Pan troglodytes	ENSPTRG00000016724	1 retrocopy	retro_ptro_692,