RetrogeneDB ID: retro_nleu_1847

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397313.1:1185132..1185592(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSNLEG00000017205
• Aliases: None
• Description: None

Sequence

>retro_nleu_1847
GCTGAGGCCATCAAGGATCTGATGCACAAGTTTTGAAGCGGCCTAGATTTTCTTCATGGCCATTGCATTGTTCACTGATA
TCTGAGGCCAGAGAACATTCTAGTGACAAGTGGTGGGACAGCCAAGCTGGCTGACTTGGTCTGGCCAGCATCTATGGCTA
CCAGATGGCGTTTACACCTGTGGTTGTTACACTCTTGTACTGTGCTCATGGGGTTCTTCTGCAATCCACACAGGCAACAT
CTGTGGACATTTGAAGTGTTAGTTTGTCTTTGCAGAGAGATTTCCTCAAAAGCCTCTCTTCTGTGGAAGCTCTAAAGCCA
ACTAGTTGGGCAAAATCTTTGACCCAATTGGGCTGCCTGTATAGGATGACTGGCCCTAAGATGTGTCTGTACCCTATGGA
GCCTTTCTCCACAGAGGGACTCACCCAGTGCAGTTGGTGGTGCCTGAGATGGAGAACAAC

Alignment

ORF - retro_nleu_1847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 50.83 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADF-GLARIYSYQMALTPVVVTLWYRA
          AE.IKDLM..F..GLDFLH..CIVH..L.PENILVTSGGT.KLAD..GLA.IY.YQMA.TPVVVTL.Y.A
Retrocopy AEAIKDLMHKF*SGLDFLHGHCIVH*YLRPENILVTSGGTAKLADL<GLASIYGYQMAFTPVVVTLLYCA

Parental  PEVLLQSTYATPVDMWSVGC-IFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFPP
          ..VLLQST.AT.VD..SV....FAE.F..KPLFCG.S.A..LGKIFD.IGLP..DDWP.DVS.P.GAF..
Retrocopy HGVLLQSTQATSVDI*SVSL<VFAERFPQKPLFCGSSKAN*LGKIFDPIGLPV*DDWP*DVSVPYGAFLH

Parental  RGPRPVQSVVPEMEES
          RG..PVQ.VVPEME..
Retrocopy RGTHPVQLVVPEMENN

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_1847 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 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000004100	1 retrocopy	retro_nleu_549,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847 ,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,