RetrogeneDB ID: retro_nleu_294

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:56705163..56705615(-)
• Located in intron of: ENSNLEG00000007420

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUNDC1
• Ensembl ID: ENSNLEG00000002513
• Aliases: None
• Description: None

Sequence

>retro_nleu_294
AACCCCGCTCCCCAAGAATATGAAAGTGATGACGACTCTTACGAAGTGTTGGATTTAACTGAGTATGCACAAAGACACCA
GTGGTGGAATCCAGTGTTTGGCCACAGTTTGGGATCTATGGTGGAAAAATACGCAGTAGCGACCCAGATTGTAATGGGTG
GCGTTCCTGGCTGGTTTGCAGCATTTTTGTTCCAGAAAGTTTGAAAACTTGCAGCAACTGCAGTAGGTGGTGACTTTCTT
GCCGTCAGATTGCTAGTCATAGTGGCTATGTGCAGATTAACTGGAAGAGAGTTGAAAAAGATGTAAACAAAGCAAAAAGG
CAGATGAAGAAACGAGCGAACAAAGCAGCACCTGAAATTAGCAATTTAATTGAAGAAGCAATAGAATTTATCAAGCAGCA
CATTGTGATATCCGGTGGATTTGTAGGAGGCTTTTTGCTCGAACTTGCATCT

Alignment

ORF - retro_nleu_294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 97.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPPPQEYESDDDFYEVLDLTEYARRHQWWNRVFGHSSGPMVEKYSVATQILMGGVTGWCAGFLFQKVGKL
          NP.PQEYESDDD.YEVLDLTEYA.RHQWWN.VFGHS.G.MVEKY.VATQI.MGGV.GW.A.FLFQKV.KL
Retrocopy NPAPQEYESDDDSYEVLDLTEYAQRHQWWNPVFGHSLGSMVEKYAVATQIVMGGVPGWFAAFLFQKV*KL

Parental  AATAVGGGFLLL-QIASHSGYVQIDWKRVEKDVNKAKRQIKKRANNAAPEINNLIEEATEFIKQNIVISS
          AATAVGG.FL...QIASHSGYVQI.WKRVEKDVNKAKRQ.KKRAN.AAPEI.NLIEEA.EFIKQ.IVIS.
Retrocopy AATAVGGDFLAV<QIASHSGYVQINWKRVEKDVNKAKRQMKKRANKAAPEISNLIEEAIEFIKQHIVISG

Parental  GFVGGFLLGLAS
          GFVGGFLL.LAS
Retrocopy GFVGGFLLELAS

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_294 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 19 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010876	1 retrocopy	retro_cjac_896,
Cavia porcellus	ENSCPOG00000012962	2 retrocopies	retro_cpor_507, retro_cpor_508,
Echinops telfairi	ENSETEG00000012763	3 retrocopies	retro_etel_1614, retro_etel_697, retro_etel_852,
Homo sapiens	ENSG00000069509	1 retrocopy	retro_hsap_936,
Gorilla gorilla	ENSGGOG00000023311	1 retrocopy	retro_ggor_755,
Latimeria chalumnae	ENSLACG00000010215	1 retrocopy	retro_lcha_74,
Macropus eugenii	ENSMEUG00000006795	5 retrocopies	retro_meug_1597, retro_meug_2127, retro_meug_232, retro_meug_415, retro_meug_994,
Microcebus murinus	ENSMICG00000000450	2 retrocopies	retro_mmur_1189, retro_mmur_1461,
Macaca mulatta	ENSMMUG00000003505	1 retrocopy	retro_mmul_38,
Monodelphis domestica	ENSMODG00000021088	3 retrocopies	retro_mdom_1262, retro_mdom_769, retro_mdom_917,
Nomascus leucogenys	ENSNLEG00000002513	2 retrocopies	retro_nleu_2760, retro_nleu_294 ,
Nomascus leucogenys	ENSNLEG00000014443	5 retrocopies	retro_nleu_1512, retro_nleu_1662, retro_nleu_1958, retro_nleu_2386, retro_nleu_494,
Oryctolagus cuniculus	ENSOCUG00000029753	5 retrocopies	retro_ocun_1008, retro_ocun_1376, retro_ocun_1567, retro_ocun_27, retro_ocun_314,
Pongo abelii	ENSPPYG00000020268	2 retrocopies	retro_pabe_806, retro_pabe_829,
Pelodiscus sinensis	ENSPSIG00000013793	1 retrocopy	retro_psin_30,
Pan troglodytes	ENSPTRG00000021821	1 retrocopy	retro_ptro_648,
Rattus norvegicus	ENSRNOG00000003470	1 retrocopy	retro_rnor_2644,
Sarcophilus harrisii	ENSSHAG00000000501	1 retrocopy	retro_shar_222,
Tarsius syrichta	ENSTSYG00000009139	1 retrocopy	retro_tsyr_1522,