RetrogeneDB ID: retro_nleu_945

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:32099855..32100142(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSNLEG00000006822
• Aliases: None
• Description: None

Sequence

>retro_nleu_945
CTCATGAGATTTTTGATGAAATGATTCATGAAACTGTAACCTTGAATTGAAAAGTGGAACACAAGTCTATGGAACAGTCA
CAAGTGTGGATATCACTGTGAATACACATCTTAAAGTGTGAAAATGACCCTGAAGACAGAGAACCTGCACAGTTGGAAAC
ACAAATTTGAGGAAGTAACATTAGATATTTTACTCTACCAGACAGTTTACCTCTGGATACACTACTTGTGGATGTTGAGC
CTAAGGTAAAACCTAAGAAAAGGGAAGCTGTTTGTTGCAGGAAGAGG

Alignment

ORF - retro_nleu_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.61 %
• Parental protein coverage: 82.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IYRFLMK-LSHETVTI-ELKNGTQLHIRFISVDVSMNTHLK-AVKMTLK-NREPVQLETLSIRGNNIRYF
          ..RFLMK...HETVT..ELK.GTQ......SVD...NTHLK..VKMTLK..REP.QLET..I.G.NIRYF
Retrocopy LMRFLMK<MIHETVTL<ELKSGTQVYGTVTSVDITVNTHLK<SVKMTLK<DREPAQLET-QI*GSNIRYF

Parental  ILPDSLPLDTLLVDVEPKVKSKKREAVAGRGR
          .LPDSLPLDTLLVDVEPKVK.KKREAV..R.R
Retrocopy TLPDSLPLDTLLVDVEPKVKPKKREAVCCRKR

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_945 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002576	1 retrocopy	retro_amel_1905,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Nomascus leucogenys	ENSNLEG00000006822	2 retrocopies	retro_nleu_2824, retro_nleu_945 ,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Otolemur garnettii	ENSOGAG00000007833	1 retrocopy	retro_ogar_3085,