RetrogeneDB ID: retro_nleu_2165

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397333.1:2520415..2520959(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAG1
• Ensembl ID: ENSNLEG00000005204
• Aliases: None
• Description: None

Sequence

>retro_nleu_2165
GAGAAGGTGACCAAGGAGGAAATAGTGGCAGCCAAGCTCAGCATGACCGTCACTCACAGCAATGAGAAGCATGACCTTCA
CGTTACCCTGCAGCAGGTCCAGCGGTGAAGCAATTGCCCAAGACCTGACCCAGGTTGTTGGAGAGGCCACAGGGGTTCCA
CTGTCTTTTCAGAAACTCATATTTAAGGGAACATCTCTGAAGGAAATGTAGATACCTTTGTCAGCATGTGGAATACAAAA
TGGTTGCCAAGTCATGTTAATTGGGAAAAAGAACAGCCCAGAGGAAGAGGTTGAACTGGAGAAATTGAAAGATTTGGTGA
AGCCTGTGGAGAAGAAAGTTGGCGAACTGTAAGAGTTGAATAAACAGCTTACTGGACTCCAGCAAGGTTTTCTGGCCAAA
GATTTGCAAACTGAAGCTTTTTGCAAACTTGATAGGAGAGGAAAAGCCACAACCGAACAGTTTATGAAGATCTTGGAAGA
GATCGACACACTGATCCTGCCAGAAAATTTCAAAGACAATAGATCAAAAAGGAAAGGTTTGGTT

Alignment

ORF - retro_nleu_2165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.82 %
• Parental protein coverage: 55.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEVTREEMAAAGLTVTVTHSNEKHDLHVTPQQ-GSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEM
          E.VT.EE..AA.L..TVTHSNEKHDLHVT.QQ..S.E...QDL.QVV.E..GVP.SFQKLIFKG.SLKEM
Retrocopy EKVTKEEIVAAKLSMTVTHSNEKHDLHVTLQQ>SSGEAIAQDLTQVVGEATGVPLSFQKLIFKGTSLKEM

Parental  ETPLSALGIQNGCRVMLIGKKNSPQEEVELKKLKHLEKSVEKIADQLEELNKELTGIQQGFLPKDLQAEA
          ..PLSA.GIQNGC.VMLIGKKNSP.EEVEL.KLK.L.K.VEK....L.ELNK.LTG.QQGFL.KDLQ.EA
Retrocopy *IPLSACGIQNGCQVMLIGKKNSPEEEVELEKLKDLVKPVEKKVGEL*ELNKQLTGLQQGFLAKDLQTEA

Parental  LCKLDRRVKATIEQFMKILEEIDTLILPENFTDSRLKRKGLV
          .CKLDRR.KAT.EQFMKILEEIDTLILPENF.D.R.KRKGLV
Retrocopy FCKLDRRGKATTEQFMKILEEIDTLILPENFKDNRSKRKGLV

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_2165 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017845	1 retrocopy	retro_btau_901,
Choloepus hoffmanni	ENSCHOG00000012656	1 retrocopy	retro_chof_2328,
Callithrix jacchus	ENSCJAG00000008074	1 retrocopy	retro_cjac_4052,
Equus caballus	ENSECAG00000017942	1 retrocopy	retro_ecab_267,
Homo sapiens	ENSG00000107262	1 retrocopy	retro_hsap_4673,
Gorilla gorilla	ENSGGOG00000016534	1 retrocopy	retro_ggor_2899,
Macaca mulatta	ENSMMUG00000020148	1 retrocopy	retro_mmul_2487,
Nomascus leucogenys	ENSNLEG00000005204	1 retrocopy	retro_nleu_2165 ,
Oryctolagus cuniculus	ENSOCUG00000008945	1 retrocopy	retro_ocun_481,
Pongo abelii	ENSPPYG00000019138	1 retrocopy	retro_pabe_3630,
Pan troglodytes	ENSPTRG00000020856	1 retrocopy	retro_ptro_3105,
Tursiops truncatus	ENSTTRG00000010573	2 retrocopies	retro_ttru_252, retro_ttru_946,