RetrogeneDB ID: retro_nleu_2577

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397374.1:3913565..3914024(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96A
• Ensembl ID: ENSNLEG00000026932
• Aliases: None
• Description: None

Sequence

>retro_nleu_2577
CTGCTCTCCTGGACACTGAGCAGGGTCCTGTGGCTCTCGGGCCTGTTTGAGTGGGGAGCTGCCCGGCAGCCCTGGATCAT
GGAAAAGAAAGTGCTAGAGGTTTATGATTTGATTCGAACTATGTGGGACCCAGAAAAGCCCAATACTTTAGAAGAACTGG
AATTGGTAGCAGAAAGTTATATGGAAGTTCAGGAGATAAATGAAGAAGACTATCTTGTTATTATCAAGTTTACACCAAGA
GTACCTCATTAATATTTGGCAATTCTTATGGGGCTGTGCTTAAGAATAAAACTTCAGCGGTGTTTATTGTTTAAACATAA
GTTGGAAATCTACATTTCTGAAGGAACCCACTTAACAGAAGATATAAGTACGCAGATAAACAACAAAGAGCAAGTGGAGG
CTGCAATGGAAAACCCCAGCTTATGGGAAATTGCGGAACAGTGTGTCCTTGAACCTGAC

Alignment

ORF - retro_nleu_2577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 96.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLSWTLSRVLWLSGLSEPGAARQPRIMEEKALEVYDLIRTIRDPEKPNTLEELEVVSESCVEVQEINEEE
          LLSWTLSRVLWLSGL.E.GAARQP.IME.K.LEVYDLIRT..DPEKPNTLEELE.V.ES..EVQEINEE.
Retrocopy LLSWTLSRVLWLSGLFEWGAARQPWIMEKKVLEVYDLIRTMWDPEKPNTLEELELVAESYMEVQEINEED

Parental  YLVIIRFTPTVPHCSLATLIGLCLRVKLQRYLPFKHKLEIYISEGTHSTEEDINKQINDKERVAAAMENP
          YLVII.FTP.VPH..LA.L.GLCLR.KLQR.L.FKHKLEIYISEGTH.T.EDI..QIN.KE.V.AAMENP
Retrocopy YLVIIKFTPRVPH*YLAILMGLCLRIKLQRCLLFKHKLEIYISEGTHLT-EDISTQINNKEQVEAAMENP

Parental  NLREIVEQCVLEPD
          .L.EI.EQCVLEPD
Retrocopy SLWEIAEQCVLEPD

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_2577 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 21 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002448	1 retrocopy	retro_amel_1707,
Bos taurus	ENSBTAG00000002012	2 retrocopies	retro_btau_509, retro_btau_984,
Canis familiaris	ENSCAFG00000017035	2 retrocopies	retro_cfam_1450, retro_cfam_439,
Callithrix jacchus	ENSCJAG00000004834	1 retrocopy	retro_cjac_1751,
Equus caballus	ENSECAG00000010303	1 retrocopy	retro_ecab_364,
Erinaceus europaeus	ENSEEUG00000000854	1 retrocopy	retro_eeur_323,
Felis catus	ENSFCAG00000004178	1 retrocopy	retro_fcat_1379,
Homo sapiens	ENSG00000166797	2 retrocopies	retro_hsap_2763, retro_hsap_522,
Gorilla gorilla	ENSGGOG00000016550	2 retrocopies	retro_ggor_1921, retro_ggor_481,
Loxodonta africana	ENSLAFG00000011114	1 retrocopy	retro_lafr_758,
Macropus eugenii	ENSMEUG00000005979	2 retrocopies	retro_meug_471, retro_meug_85,
Microcebus murinus	ENSMICG00000011072	1 retrocopy	retro_mmur_233,
Myotis lucifugus	ENSMLUG00000028233	2 retrocopies	retro_mluc_578, retro_mluc_893,
Mustela putorius furo	ENSMPUG00000000605	1 retrocopy	retro_mputfur_722,
Mus musculus	ENSMUSG00000032381	1 retrocopy	retro_mmus_1919,
Nomascus leucogenys	ENSNLEG00000026932	3 retrocopies	retro_nleu_156, retro_nleu_2577 , retro_nleu_667,
Ochotona princeps	ENSOPRG00000015229	5 retrocopies	retro_opri_476, retro_opri_522, retro_opri_828, retro_opri_84, retro_opri_999,
Pongo abelii	ENSPPYG00000006544	1 retrocopy	retro_pabe_224,
Pan troglodytes	ENSPTRG00000007153	2 retrocopies	retro_ptro_1870, retro_ptro_390,
Sorex araneus	ENSSARG00000002068	3 retrocopies	retro_sara_54, retro_sara_597, retro_sara_742,
Tarsius syrichta	ENSTSYG00000004186	2 retrocopies	retro_tsyr_195, retro_tsyr_62,