RetrogeneDB ID: retro_nleu_2081

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397327.1:3637535..3638304(+)
• Located in intron of: ENSNLEG00000001705

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC4
• Ensembl ID: ENSNLEG00000015607
• Aliases: None
• Description: None

Sequence

>retro_nleu_2081
ATGGACTTCCTAGTTCTCTTCCAGCTCTACTGGCTTTGGCGCTAGTTGGTTATGTTACGATCTGTTTTTGCTAGAAAACT
CATGATTTGAAATGCCTGGTCAGGGCAGGAGCACAGATATTTTCCTATATAATTCCAGAATGTCTTCAGAAAGCCATGTA
AAAATTGCTTCATTACCTCTTCCATACATGAAACCATACCTTCATTATCCTTCACCTGGTCTTGCAAGGGATGGTAAATA
CTGAATATACCTGGGAAATACTTGGCTACTGTCTAAAGCTAGTTCTCCTGTATTACCTTCTTCTGCCCTATCTGCTTCTG
ATTGTAAACCCATTTATTTCCACCCTAACTTGTGTAACTGATTCTGGCATTATAAGAAAAGCAAATGAATTATTTCTTCA
AATTTATGAATTCGATGAAGTGATGTTTCTAAAGAGGTGAGGTGCTCTACTTATGATTTACGAACACCAGCTCGATCTAA
GCACTGACTGCAGTGTGTGCGCCGTTTTGACCATCATTGGGTTTGGGTGAACAACTGCATCTGGGCTTGGAACACCAGTT
ATTAATACTTTCTCATCTACCTCTTGATGTTGGCGGCCTCGGCTGCTGCCATGGCCATTGTGAGCACTGCATTTCTGGTC
GACTTGGTGGTATTGTTGGATTTGTACTAGACTTACATTGATGACCTTGGACACTTCCAGTTTATGGACTTGATTTTTCT
TATTCAGTACCTGTTCCTGACCTTTCCAACAATTGTCTTCATGCTGGGG

Alignment

ORF - retro_nleu_2081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.08 %
• Parental protein coverage: 75.87 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDFLVLFLFY-LASVLMGLVLICVCSKTHSLKGLARGGAQIFSCIIPERLQRAVHGLLHYLFHTRNHTFI
          MDFLVLF..Y.LA..L.G.V.IC.C.KTH.LK.L.R.GAQIFS.IIPE.LQ.A...LLHYLFHT.NHTFI
Retrocopy MDFLVLFQLY<LALALVGYVTICFC*KTHDLKCLVRAGAQIFSYIIPECLQKAM*KLLHYLFHT*NHTFI

Parental  VLHLVLQGMVYTEYTWEVFGYCQELEFSLYYLLLPYLLLVVNLFSFTLTCVTNPGIITKANELLFLHVYE
          .LHLVLQGMV.TEYTWE..GYC..L...LYYLLLPYLLL.VN.F..TLTCVT..GII.KANE.LFL..YE
Retrocopy ILHLVLQGMVNTEYTWEILGYCLKLVL-LYYLLLPYLLLIVNPFISTLTCVTDSGIIRKANE-LFLQIYE

Parental  FDEVMF-PKNVRCSTCDLRKPARSKHCSVCNWCVHRFDHHCVWVNNCIGAWNIR--YFLIYLLTLTASAA
          FDEVMF..K.VRCST.DLR.PARSKH...C...V.RFDHH.VWVNNCI.AWN....YFLIYLL.L.ASAA
Retrocopy FDEVMF<SKEVRCSTYDLRTPARSKH*LQC---VRRFDHHWVWVNNCIWAWNTSY*YFLIYLLMLAASAA

Parental  TVAIVSTTFLVHLVVMSDLYQETYIDDLGHLHVMDTVFLIQYLFLTFPRIVFMLG
          ..AIVST.FLV.LVV..DLY..TYIDDLGH...MD..FLIQYLFLTFP.IVFMLG
Retrocopy AMAIVSTAFLVDLVVLLDLY-*TYIDDLGHFQFMDLIFLIQYLFLTFPTIVFMLG

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_2081 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009547	1 retrocopy	retro_btau_643,
Dasypus novemcinctus	ENSDNOG00000009165	1 retrocopy	retro_dnov_2610,
Homo sapiens	ENSG00000136247	1 retrocopy	retro_hsap_1193,
Macaca mulatta	ENSMMUG00000015545	1 retrocopy	retro_mmul_1283,
Nomascus leucogenys	ENSNLEG00000015607	1 retrocopy	retro_nleu_2081 ,
Pongo abelii	ENSPPYG00000017352	1 retrocopy	retro_pabe_993,
Pan troglodytes	ENSPTRG00000018915	1 retrocopy	retro_ptro_3038,
Pteropus vampyrus	ENSPVAG00000016104	2 retrocopies	retro_pvam_1175, retro_pvam_758,
Ictidomys tridecemlineatus	ENSSTOG00000011605	1 retrocopy	retro_itri_1054,
Tursiops truncatus	ENSTTRG00000005001	1 retrocopy	retro_ttru_179,
Vicugna pacos	ENSVPAG00000011480	1 retrocopy	retro_vpac_177,