RetrogeneDB ID: retro_nleu_1352

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397290.1:4941584..4942344(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALG3
• Ensembl ID: ENSNLEG00000006230
• Aliases: None
• Description: None

Sequence

>retro_nleu_1352
CTCAGTATCAGCCTCCTGCTGGTCCAGCACTGGGGCTGGGGCTGCTGGTGTTCCAGCCTGGCAGCCTCTGTGAAGATGAA
TGTGCTGCTCTTCACCCTGGGTTACTGTTTCTTCTCCTCACACAGTTTGGCTGCCATGGGGCCTTCCCCAAGCTGGGCAT
CTGTGTTGGCCTTCAGGTGGTGCTGGGGTTGCCCTTCCTGCTGGAGAAGCCCACTGGCTACCTGTCTCGCTCCTTTGACC
TTGGCCGCCAGTTTCTGTTCTGCTGGACAGTGAACCGGTGCTTCCTCCCAGGGGCTCTCTGCCTGCACCGTGACTTCCAC
CTCGCCCTGCTGGCCACCTCACCTTGCTCTACTGGTGGGTGTTTACCCTCTACTGGTGGCACAGGATGGGGGAATGTATC
TTGTCACTGCTGAAGGATCCCTCCAAAAGGAAGGTTCCACCCCAGCCCTTCACACCTAACCAGATCGTTTCTGCCCTCTT
CACCTCTAACTTCGTTGGCATCTGCTTCAGCCACCCACTCCACTACCAGTTCTATGTCTGGTATTTCCACACACTGCCCT
ACCTCCTGCGGGCCAGGACTGCACACTGGCTCACACACCTGCTCAGGTTGCTGGTGGTGGGGCTCATGGAGCTCTCCTGG
AACACATACCCCTCCACATCCTGCAGCTCTGCTGCCCAGCCTGTGTGCCGTGCTGTCCTCCTGCTGCAGCTCTGGCTGGG
CCTGCAGCCATTCCCCAAGAGCATCCAACACAGCAAGAAA

Alignment

ORF - retro_nleu_1352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.3 %
• Parental protein coverage: 57.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSINLLLAQRWGWGCCFFSLAVSVKMNVLLFA-PGLLFLLLTQFGFRGALPKLGICAGLQVVLGLPFLLE
          LSI.LLL.Q.WGWGC...SLA.SVKMNVLLF..PGLLFLLLTQFG..GA.PKLGIC.GLQVVLGLPFLLE
Retrocopy LSISLLLVQHWGWGCWCSSLAASVKMNVLLFT<PGLLFLLLTQFGCHGAFPKLGICVGLQVVLGLPFLLE

Parental  NPIGYLSRSFDLGRQFLFRWTVNWRFLPEALFLHRAFHLALLTA-HLTLLL-LFALCRWHRTGESILSLL
          .P.GYLSRSFDLGRQFLF.WTVN..FLP.AL.LHR.FHLALL...HL.LL...F.L..WHR.GE.ILSLL
Retrocopy KPTGYLSRSFDLGRQFLFCWTVNRCFLPGALCLHRDFHLALLAT>HLALLV>VFTLYWWHRMGECILSLL

Parental  RDPSKRKVPPQPLTPNQIVSTLFTSNFIGICFSRSLHYQFYVWYFHTLPYLLWATPARWLTHLLRLLVLG
          .DPSKRKVPPQP.TPNQIVS.LFTSNF.GICFS..LHYQFYVWYFHTLPYLL.A..A.WLTHLLRLLV.G
Retrocopy KDPSKRKVPPQPFTPNQIVSALFTSNFVGICFSHPLHYQFYVWYFHTLPYLLRARTAHWLTHLLRLLVVG

Parental  LIELSWNTYPSTSCSSAALHICHAVILLQLWLGPQLFPKSTQHSKK
          L.ELSWNTYPSTSCSSAA...C.AV.LLQLWLG.Q.FPKS.QHSKK
Retrocopy LMELSWNTYPSTSCSSAAQPVCRAVLLLQLWLGLQPFPKSIQHSKK

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_1352 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000214160	1 retrocopy	retro_hsap_3286,
Macaca mulatta	ENSMMUG00000018951	1 retrocopy	retro_mmul_2063,
Nomascus leucogenys	ENSNLEG00000006230	1 retrocopy	retro_nleu_1352 ,
Pongo abelii	ENSPPYG00000014350	1 retrocopy	retro_pabe_2715,