RetrogeneDB ID: retro_nleu_1205

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:19731536..19731780(-)
• Located in intron of: ENSNLEG00000004487

Retrocopy information

• Ensembl ID: ENSNLEG00000004562
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PHF5A
• Ensembl ID: ENSNLEG00000015481
• Aliases: None
• Description: None

Sequence

>retro_nleu_1205
ATGGCTAAACATCATCCCGATTTGATCTTTTGCTGCAAGCAGACTGGTATTGCTATCAGAAGACTGTGTGAAAAATGTGA
TGGCAAGTGTGTGATTTGTGATTCCTATGTGCGTCCCTGCGCTCTGATGCACATATGTGATGAGCGTAACTATGGATCTT
ACCACGGGTGCTGTGTGATCTGTGGAGGCCCTGGGGTTTCTGATGCCTGTTATTGTAAGGAAGTGCACCATCCAGGAGGA
GGAT

Alignment

ORF - retro_nleu_1205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAY
          MAKHHPDLIFC.KQ.G.AI.RLCEKCDGKCVICDSYVRPC.L..ICDE.NYGSY.G.CVICGGPGVSDA.
Retrocopy MAKHHPDLIFCCKQTGIAIRRLCEKCDGKCVICDSYVRPCALMHICDERNYGSYHGCCVICGGPGVSDAC

Parental  YCKE-CTIQEKD
          YCKE.CTIQE.D
Retrocopy YCKE>CTIQEED

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_1205 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015687	1 retrocopy	retro_amel_1674,
Canis familiaris	ENSCAFG00000001090	1 retrocopy	retro_cfam_369,
Callithrix jacchus	ENSCJAG00000004999	3 retrocopies	retro_cjac_1194, retro_cjac_1527, retro_cjac_906,
Echinops telfairi	ENSETEG00000010741	1 retrocopy	retro_etel_102,
Latimeria chalumnae	ENSLACG00000012094	1 retrocopy	retro_lcha_25,
Microcebus murinus	ENSMICG00000013520	1 retrocopy	retro_mmur_758,
Mustela putorius furo	ENSMPUG00000016398	2 retrocopies	retro_mputfur_359, retro_mputfur_439,
Mus musculus	ENSMUSG00000061360	3 retrocopies	retro_mmus_1070, retro_mmus_1071, retro_mmus_1155,
Nomascus leucogenys	ENSNLEG00000015481	2 retrocopies	retro_nleu_1205 , retro_nleu_653,
Oryctolagus cuniculus	ENSOCUG00000012705	1 retrocopy	retro_ocun_640,
Otolemur garnettii	ENSOGAG00000002839	1 retrocopy	retro_ogar_55,
Pteropus vampyrus	ENSPVAG00000001162	1 retrocopy	retro_pvam_66,
Rattus norvegicus	ENSRNOG00000024170	3 retrocopies	retro_rnor_2660, retro_rnor_2704, retro_rnor_2712,
Tarsius syrichta	ENSTSYG00000001082	1 retrocopy	retro_tsyr_259,
Tursiops truncatus	ENSTTRG00000003369	1 retrocopy	retro_ttru_1483,