RetrogeneDB ID: retro_nleu_176

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:32735121..32735414(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK2AP2
• Ensembl ID: ENSNLEG00000006438
• Aliases: None
• Description: None

Sequence

>retro_nleu_176
AGCCTCTCATCACCGTAGGGCTCAGTGTCAGGAGTCGCTGCCCCTTTCAGACCGCTGTTTAACGACTTTGGACCGCCTTC
CATGGGCTATGTGCAGGCGATGAAGCCACTGGCACCCAGGGCTCCCAGAGCACCTACAAGGACCTGCTGTCGGTCATAGA
GGAGATGGGCAAAGAGATCCGGCCTGCCTATGCTGGCAGCAAGAGCACCATGGAGCGCCTGAAGAGAGGTATCATCCATG
CCCAGGCCCTAGTCAGAGAGTGCCTGGCAGAGACAGAGTGGAACGCCCGCACG

Alignment

ORF - retro_nleu_176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.86 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVPSPSGSVPGAGAPFRPLFNDFGPPSMGYVQAMKP-PGAQGSQSTYTDLLSVIEEMGKEIRPTYAGSKS
          S..SP.GSV.G..APFRPLFNDFGPPSMGYVQAMKP..G.QGSQSTY.DLLSVIEEMGKEIRP.YAGSKS
Retrocopy SLSSP*GSVSGVAAPFRPLFNDFGPPSMGYVQAMKP<TGTQGSQSTYKDLLSVIEEMGKEIRPAYAGSKS

Parental  AMERLKRGIIHARALVRECLAETERNART
          .MERLKRGIIHA.ALVRECLAETE.NART
Retrocopy TMERLKRGIIHAQALVRECLAETEWNART

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_176 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011370	1 retrocopy	retro_cfam_55,
Equus caballus	ENSECAG00000020079	2 retrocopies	retro_ecab_180, retro_ecab_579,
Echinops telfairi	ENSETEG00000006428	3 retrocopies	retro_etel_257, retro_etel_334, retro_etel_437,
Homo sapiens	ENSG00000167797	4 retrocopies	retro_hsap_3699, retro_hsap_4172, retro_hsap_4176, retro_hsap_4268,
Gorilla gorilla	ENSGGOG00000010159	3 retrocopies	retro_ggor_2502, retro_ggor_2799, retro_ggor_2800,
Macaca mulatta	ENSMMUG00000011827	5 retrocopies	retro_mmul_1712, retro_mmul_640, retro_mmul_728, retro_mmul_730, retro_mmul_763,
Nomascus leucogenys	ENSNLEG00000001478	2 retrocopies	retro_nleu_1209, retro_nleu_2686,
Nomascus leucogenys	ENSNLEG00000006438	1 retrocopy	retro_nleu_176 ,
Otolemur garnettii	ENSOGAG00000008275	1 retrocopy	retro_ogar_1584,
Pan troglodytes	ENSPTRG00000003966	9 retrocopies	retro_ptro_2508, retro_ptro_2973, retro_ptro_2976, retro_ptro_3002, retro_ptro_3003, retro_ptro_3004, retro_ptro_3005, retro_ptro_3008, retro_ptro_3009,
Tupaia belangeri	ENSTBEG00000005476	2 retrocopies	retro_tbel_439, retro_tbel_612,