RetrogeneDB ID: retro_nleu_907

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:11784723..11785115(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF1
• Ensembl ID: ENSNLEG00000000752
• Aliases: None
• Description: None

Sequence

>retro_nleu_907
TCCCAAGGTTTGGACTGGGTCACCCAGCCCAGTTGGGAAGAGCCAGCAGTGAGCAACCTTGGCATCCCCTTCAGCAGCTT
TGACCACTCTAAAGCCCCCTACTATGGCTATGATGAGCAGCTGAGCCTGTGCCCAGAGTGGCTGAGTTCTGGCAAAGACG
AGAATAAAAGCATCCTGCAGAACAAGTATGTCCGATGTTCTGTTAGAACTGAGGTATGCCATCTCTGGATGGTCCTGTGT
CACCGCTTGATGCTAAATCCTCAGCATGTGCAGCTCCTTTTTGACAATGAAGTTCTCCCTGATCACACGACAATGAAGCA
GCTATGACTCTCCGCTGGTTCGACAAGCTATCCCCTTTGCTTTTACAATACAGTATGAAAGAGAACAGGAGG

Alignment

ORF - retro_nleu_907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 50.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRGLDRVTQPSGEEPALSNLGLPFSSFDHSKAHYYRYDEQLNLCLERLSSGKDKNKSVLQNKYVRCSVRA
          S.GLD.VTQPS.EEPA.SNLG.PFSSFDHSKA.YY.YDEQL.LC.E.LSSGKD.NKS.LQNKYVRCSVR.
Retrocopy SQGLDWVTQPSWEEPAVSNLGIPFSSFDHSKAPYYGYDEQLSLCPEWLSSGKDENKSILQNKYVRCSVRT

Parental  EVRHLRRVLCHRLMLNPQHVQLLFDNEVLPDHMTMKQIWLS-RWFGKPSPLLLQYSVKEKRR
          EV.HL..VLCHRLMLNPQHVQLLFDNEVLPDH.TMKQ..LS.RWF.K.SPLLLQYS.KE.RR
Retrocopy EVCHLWMVLCHRLMLNPQHVQLLFDNEVLPDHTTMKQL*LS<RWFDKLSPLLLQYSMKENRR

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_907 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000115289	1 retrocopy	retro_hsap_1029,
Mus musculus	ENSMUSG00000069678	1 retrocopy	retro_mmus_2722,
Nomascus leucogenys	ENSNLEG00000000752	1 retrocopy	retro_nleu_907 ,
Nomascus leucogenys	ENSNLEG00000000926	1 retrocopy	retro_nleu_1826,
Pongo abelii	ENSPPYG00000012270	1 retrocopy	retro_pabe_862,
Pan troglodytes	ENSPTRG00000012094	1 retrocopy	retro_ptro_704,
Sorex araneus	ENSSARG00000007319	1 retrocopy	retro_sara_448,
Sus scrofa	ENSSSCG00000008277	1 retrocopy	retro_sscr_1069,