RetrogeneDB ID: retro_nleu_766

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397272.1:16499682..16500672(-)
• Located in intron of: ENSNLEG00000005731

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEIL2
• Ensembl ID: ENSNLEG00000015054
• Aliases: None
• Description: None

Sequence

>retro_nleu_766
ATGCTAGAAGGGCTGTTGGTGAGGACATTTCACCATTTGGTCTCTCCTTTTGTGGGCAAGCAGGTGGTCAAGATAGGGAG
CAACAGTAAGAAGCTATAGCCCACCAGCCTCCAGTCTCTGTGGCTCCAGGACAGCCAGGTCCATGGAAAGAAATTATTCC
TTAGATTTGATCCAGACGAAGAAATGGAGCCCGTTGGCAACAGCCCACCGCCAGAGCCTCCACAAAAAGAAGCACAGAAG
GAAGGGACTGCGGACTCAAAGTAGGCCTGGGAGCCCCGTGGGCAGAAGACCCTTGATGCCTCCTCATGGTCCACAGAGCT
CGTCCTCCAGGGAGAGGATGATGAGGAATGTTTGAAGGGAGACACCCCTACAGGAGATGCTGGGAGGTGGCTGCGTGTCA
GCTCGTTTGTTGGCAGCGTTTGGGTGAACGACTTCTCCAGATCCAAGAAAGCCAACAAGGAGGGGACTGGAGGGACCCTG
CCCCGAGGTTGGTCGTGTACTTTGGTGGTGGTGGCTTCCTGGCATTTTATAATTGTCAGATGTCTTGGAGCTCTTCCCCA
GAGGTCACACCCACCTGTGACATCCTGTCTGAGAAGTTCCATTGAGGACAAGCCTTGGAAGCGCTAGGCCAGGCTCAGCC
TGTCTGTTATACACCATTGGACCAGAAATACTTCTCAGGGCTAGGGAACATCATTAAGAATGAAGTCTTGTACAGAGCTG
GCATCCATCCCCTTTCTCTTGGTTCAGTCCTGAGTGCCTCCACGTTAGGAGGCCCTGGTGGATCACGTGGTGGAGTTCAG
TACAGCCTGGCTGCAGGGCAAGTTCCAGGGCAAACTGCAGCACATGCAGGTCTACCAGAAAGAACAGTTCCCTGCTGGCC
ACCAGGTCATGAAGAAGCCCTTTGGGCCCTCAGGTGGGTTCCAGAGGCTCACCTGGTGGTGCCCACAGTGCCAGCCTCAG
TTGTCAGAGGAGCCAGAGCAGTGCCAGTTC

Alignment

ORF - retro_nleu_766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.18 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPEGPLVRKFHRLVSPFVGQQVVKTGGSSKKLQPASLQSLWLQDTQVHGKKLFLRFDPDEAMGPPGSSPP
          M.EG.LVR.FH.LVSPFVG.QVVK.G..SKKL.P.SLQSLWLQD.QVHGKKLFLRFDPDE.M.P.G.SPP
Retrocopy MLEGLLVRTFHHLVSPFVGKQVVKIGSNSKKL*PTSLQSLWLQDSQVHGKKLFLRFDPDEEMEPVGNSPP

Parental  PEPPQKEAQNEGAADPMQVGEPSGQKTPDGSSQSAELGPQGEDDSEYLERDAPAGDAGRWLCVSFGLFGS
          PEPPQKEAQ.EG.AD.....EP.GQKT.D.SS.S.EL..QGEDD.E.L..D.P.GDAGRWL.VS....GS
Retrocopy PEPPQKEAQKEGTADSK*AWEPRGQKTLDASSWSTELVLQGEDDEECLKGDTPTGDAGRWLRVS-SFVGS

Parental  VWVNEFSRAKKANKRG-DWRDPSPRLVLHFGGGGFVAFYNCQMSWSSSPVVTPTCDILSEKFHRGQALEA
          VWVN.FSR.KKANK.G.DWRDP.PRLV..FGGGGF.AFYNCQMSWSSSP.VTPTCDILSEKFH.GQALEA
Retrocopy VWVNDFSRSKKANKEG<DWRDPAPRLVVYFGGGGFLAFYNCQMSWSSSPEVTPTCDILSEKFH*GQALEA

Parental  LGQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSAS-RREVLVDHVVEFSTAWLQGKFEG
          LGQAQPVCYT.LDQ.YFSGLGNIIKNE.LYRAGIHPLSLGSVLSAS.R.E.LVDHVVEFSTAWLQGKF.G
Retrocopy LGQAQPVCYTPLDQKYFSGLGNIIKNEVLYRAGIHPLSLGSVLSAS>R*EALVDHVVEFSTAWLQGKFQG

Parental  KPQHTQVYQKEQCPAGHQVMKEAFGPQNGLQRLTWWCPQCQPQLSEEPEQRQF
          K.QH.QVYQKEQ.PAGHQVMK..FGP..G.QRLTWWCPQCQPQLSEEPEQ.QF
Retrocopy KLQHMQVYQKEQFPAGHQVMKKPFGPSGGFQRLTWWCPQCQPQLSEEPEQCQF

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_766 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000154328	1 retrocopy	retro_hsap_3111,
Macaca mulatta	ENSMMUG00000019209	1 retrocopy	retro_mmul_1982,
Nomascus leucogenys	ENSNLEG00000015054	1 retrocopy	retro_nleu_766 ,
Pongo abelii	ENSPPYG00000018348	1 retrocopy	retro_pabe_2569,
Pan troglodytes	ENSPTRG00000019995	1 retrocopy	retro_ptro_2103,