RetrogeneDB ID: retro_nleu_1629

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397302.1:604164..604770(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSNLEG00000013800
• Aliases: None
• Description: None

Sequence

>retro_nleu_1629
ATGTCTCAGGAACCTGCCCCACCTCTACCTAGAGATAAGTCTTCTTGTCCCATAGTAGAAAGCTAGTGTTATATACAGAT
CAAAATAGTAAAATATTCAACATATAGACAATTAATAACTTCAGTTTTTGTCAAGAGGAAATGGGTGAGGAGTCAAAAAA
TTCCAAATTTTCACCTGGCCCAAATGACAAAACTAAATGGTGCCTGAGGGTAAACCCAAAGGAATTAAATAATGAAAGTA
AAGACTACTTGGTCCTTATATTTGCTTTTAGTCAGATGCCCCAAAAGTGAAGTGTGAGCAAAATTCAAATGTTCCCTTCT
GAATGCTAAAAGGGAAGAAACAAAAGCAATGGAAAGCCAAAGAGCATATCAATTTGTGCAAGGGAAGGACTGGGATTTTT
AAAAATTCATTAGAAGAGAACTTTTGATTGATGAAACTAATAGTCTTTGACCAGATGACAAGCTTACATTATTTTACGAG
ATGAGTGTTATCCAAGATTCAGTAAACAAATCAGGACATATTAATACAAATACTTTGAAGGTGCCTGAGGGTCACCTAGG
AGAAGACTGAGGTAATCTCTGGGAAAACACAAGATTTATTGACTGC

Alignment

ORF - retro_nleu_1629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.49 %
• Parental protein coverage: 51.53 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSREPTPPLPGDMSTGPIAESWCYTQVKVVKFSY-MWTINNFSFCREEMGEVLKSSTFSSGPSDKMKWCL
          MS.EP.PPLP.D.S..PI.ES.CY.Q.K.VK.S....TINNFSFC.EEMGE..K.S.FS.GP.DK.KWCL
Retrocopy MSQEPAPPLPRDKSSCPIVES*CYIQIKIVKYST<I*TINNFSFCQEEMGEESKNSKFSPGPNDKTKWCL

Parental  RVNPKGLDDESKDYL-SLYLLLVSCPKSEVRAKFKFSLLNAKREETKAMESQRAYRFVQGKDWGFKKFIR
          RVNPK.L..ESKDYL.SLYLLLV.CPKSEV.AKFK.SLLNAKREETKAMESQRAY.FVQGKDW.F.KFIR
Retrocopy RVNPKELNNESKDYL>SLYLLLVRCPKSEV*AKFKCSLLNAKREETKAMESQRAYQFVQGKDWDF*KFIR

Parental  RDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDC
          R..L.DE.N.L.PDDKLTLF.E.SV.QDSVN.SGH.NTNTLKVPE..L.ED.GNLWENTRF.DC
Retrocopy RELLIDETNSL*PDDKLTLFYEMSVIQDSVNKSGHINTNTLKVPEGHLGED*GNLWENTRFIDC

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_1629 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629 ,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440, retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054,