RetrogeneDB ID: retro_nleu_819

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397273.1:37493591..37494355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000009512
• Aliases: None
• Description: None

Sequence

>retro_nleu_819
ATATCTGCATGTATTCAGGTAACCAGAGATGAGAATTATGAGCCCATTGAAATACCATCAGAAGATGATGGAACGGTGCT
GCTGCCCATGGTTACAGTCCAGTTTCCAGGGGCATGTGGGTTTCCCTACAGGATTCCAGTGTCTCAGGTATTAGGGGTGT
CTGCTGGTAGAAGGAATTCTGCATGCCCCCAATGCTGGCTGGGGAAATTTGATATACGTTGTTAACTATTCTGTAGATAA
CTACAGAAAAAGGGATAAGACAGATACTTCATTAGCCATAAAAGTGAAAAGAGTAGTCCAGAAAACATCTGCTTTAGTAG
TGTTGAGTCTCCCGTGGAAAACAACTGAACACGATCTGAAAGAATGTTTCAGTACCTTCAGAGAAATTCTTATGGTTCAG
GTCAAGAAGGATGTTAGAACTGGCTATTCAAAGGGGTTTGGCTTTGTTTATTTTATAAAATATGAAACCCAGGTGAAAGA
ATGTCACAGCAACATAAGACAGATAGATTATGGTGTGACTCTACAATTCCTAACTCTAAGCAAACCCTGAATGAGACTTT
GAGAAGCAAAAAGATGTTTGTGGGGTGTTGTACAGACAACATGAATTCTGATAAACTGCAGCAGTTCTTTTGTCATTGCA
GAGAAGTGATAGATGTCTTCAATTCCAAACCATTCAGGGACTTTGACTTTCTTACATTGCAGATGTTTAGCTTGCCCAGT
CTCTTTGTGGACAGGACTTGATTATTAAGGGAATCAGCATACAT

Alignment

ORF - retro_nleu_819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.08 %
• Parental protein coverage: 95.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCM-RGV-RLVEGILHAPDAGW
          .S..I.VT.DEN.EPIEIPSEDDGTVLL..VT.QFPGACG..YR.PVSQ...RGV..LVEGILHAP.AGW
Retrocopy ISACIQVTRDENYEPIEIPSEDDGTVLLPMVTVQFPGACGFPYRIPVSQVL<RGV<LLVEGILHAPNAGW

Parental  GNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD
          GNL.YVVNY..DN.RK.D.TD.S.A.KVKR.VQKTS.L.VL.LPWKTTE.DLKE.FSTF.E.LMVQVKKD
Retrocopy GNLIYVVNYSVDNYRKRDKTDTSLAIKVKRVVQKTSALVVLSLPWKTTEHDLKECFSTFREILMVQVKKD

Parental  LKTGHSKGFGFVRFTEYETQVKV-MSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCTEDMTEDEL
          ..TG.SKGFGFV.F..YETQVK..MSQ.H..D..WCD...PNSKQ...E.LRS.K.FVG.CT..M..D.L
Retrocopy VRTGYSKGFGFVYFIKYETQVKE<MSQQHKTDRLWCDSTIPNSKQTLNETLRSKKMFVGCCTDNMNSDKL

Parental  REFFSQYGDVMDVFIPKPFRAFAFVT-FADDQIAQSLCGEDLIIKGISVH
          ..FF.....V.DVF..KPFR.F.F.T..AD...AQSLCG.DLIIKGIS.H
Retrocopy QQFFCHCREVIDVFNSKPFRDFDFLT<IADV*LAQSLCGQDLIIKGISIH

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_819 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002381	2 retrocopies	retro_cjac_2457, retro_cjac_525,
Dasypus novemcinctus	ENSDNOG00000008531	1 retrocopy	retro_dnov_2262,
Homo sapiens	ENSG00000120948	2 retrocopies	retro_hsap_1209, retro_hsap_3637,
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847,
Mus musculus	ENSMUSG00000041459	1 retrocopy	retro_mmus_1958,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819 ,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008,
Pan troglodytes	ENSPTRG00000000136	2 retrocopies	retro_ptro_2460, retro_ptro_828,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652,
Tarsius syrichta	ENSTSYG00000004077	1 retrocopy	retro_tsyr_2004,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17,