RetrogeneDB ID: retro_nleu_297

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:1401014..1401431(+)
• Located in intron of: ENSNLEG00000002914

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTC
• Ensembl ID: ENSNLEG00000012929
• Aliases: None
• Description: None

Sequence

>retro_nleu_297
GTCCCTGAATGTCCCAACCTGAAGCTGAAGAAGCCACCATGACTGCACATGGCATTGGCCATGACTGTGTATGCTCTGGT
GGTGGTGTCTTACTTCCTCACCACTGGAGGAATAATTTATGATGTTATTGTTGAACCTGCAAGTGTTGGCTCTATGACTG
ATGAACATAGGCATTAGAGGCCAGTAGCTTTCTTGGCCTACAGAGTAAATGGACAATATATTATGGAAGGACTTGCATCC
AGCTTCCTGTTTACAATGGGAGGTTTACGTTTCATAATCCTGGACCAATTGAATGCACCAAATATCCCAAAACTCAATAG
ATTTCTTTTTCTATTCATTAAATTCATCTGTGTCCTATTGAGTTTTTTCATGGCTAGAGTTTTCATGAGAATGAAAGTGC
TGGGCTATCTGAAGGGT

Alignment

ORF - retro_nleu_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.77 %
• Parental protein coverage: 93.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQRPVAFLAYRVN
          V.ECPNLKLKKPP.LHM..AMTVYALVVVSYFL.TGGIIYDVIVEP.SVGSMTDEH.H.RPVAFLAYRVN
Retrocopy VPECPNLKLKKPP*LHMALAMTVYALVVVSYFLTTGGIIYDVIVEPASVGSMTDEHRH*RPVAFLAYRVN

Parental  GQYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLLSFFMARVFMRMKLPGYLMG
          GQYIMEGLASSFLFTMGGL.FIILD..NAPNIPKLNRFL.LFI.F.CVLLSFFMARVFMRMK..GYL.G
Retrocopy GQYIMEGLASSFLFTMGGLRFIILDQLNAPNIPKLNRFLFLFIKFICVLLSFFMARVFMRMKVLGYLKG

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_297 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 9 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Loxodonta africana	ENSLAFG00000026381	7 retrocopies	retro_lafr_1046, retro_lafr_17, retro_lafr_222, retro_lafr_231, retro_lafr_444, retro_lafr_549, retro_lafr_618,
Nomascus leucogenys	ENSNLEG00000012929	11 retrocopies	retro_nleu_1372, retro_nleu_1436, retro_nleu_2026, retro_nleu_2265, retro_nleu_2274, retro_nleu_2665, retro_nleu_2796, retro_nleu_2826, retro_nleu_297 , retro_nleu_474, retro_nleu_923,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Otolemur garnettii	ENSOGAG00000033684	1 retrocopy	retro_ogar_578,
Pan troglodytes	ENSPTRG00000024222	1 retrocopy	retro_ptro_34,
Rattus norvegicus	ENSRNOG00000023322	1 retrocopy	retro_rnor_2297,
Ictidomys tridecemlineatus	ENSSTOG00000021644	6 retrocopies	retro_itri_1211, retro_itri_1386, retro_itri_15, retro_itri_1571, retro_itri_789, retro_itri_863,