RetrogeneDB ID: retro_nleu_872

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:30196367..30197388(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000015748
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AGAP1
• Ensembl ID: ENSNLEG00000010626
• Aliases: None
• Description: None

Sequence

>retro_nleu_872
CCCACCTCCCCTCACACCAACAGAAAGAAGCACCGTAGGCAGAAAACCACCAGCAACTTCAAAGCCGATGGTCTGTCTGG
CACTGCTGAAGAACAAGAAAACTTTGAGTTTATCATTGTGTCCCTCACTGGCCAAACGTGGCACTTTGAAGCCACGACGA
ATGAGGAGCGGGACACCTGGGTCCAAGCCATCGAGAGCCAGATTCTGGCCAGCCTGCAGTCGTGCAAGAGCAGTAAGAAC
AAGTCCCAGCTGATGAACCAGAGTGAGGCCATGGCCCTGCAGTCAATCTGATACACGCACGGGAACTCCCACTGTGTGGA
CTTCGAGACCCAGAATCCTAACTGGGCCAGTTTGAACTTGGGAGCGCTCATGTGCATCTAGTGCTTAGGGATCCACTGGA
ATCTTGGCACTCACCTTTCCCTGAGTCTGATCTCTGGACCAGGATGACTGGCCAGTTGAGCTTATCAAGATGATGTCACC
CATTGGGAACGAGCTACTCAACAGCGTCTGGGAAGAGAGCAGCCAGGGGCAGACGAAACCCTTAGTAGACTCCACAAGGG
AAGAGAAGGAACAATGGATCCATGCCAAGTACGAGCAGAAGCTCTTCCTGGCCCCGCTACCCTGCACGGATCTGTCCCTG
GGTCAGCATCTGCTTCGGGCCACCGCAGACGAGGACCTGTGGACGGCCATCCTGCTGCTGGTGCATGGCTCCCGGGACGA
GGCGAAAGAAACCTTCCGGGAGGGAGACTGAGATGGCTGCCCTGCACTGCATCTGGCCTGCCACAAGGGAAATGTGGTCC
TGGTGCAGCTCCTGATCTGGTACGGGGTGGACGTCATGGCCTGAGATACCCATGGGAACACAGTGCTGGCCTACACCTGG
CAGGCCTCCAGGCAGGAATGCATCAATGTGCTGCTGGAGTATGGCTGCCCCGATGAGCGCTGAGTGCTCATGGCCATCCC
TAACTTGTCCAGGAGAAACAATAACCGGAACAGCAGCAGCAGGAGGGTGCCCACCATCATC

Alignment

ORF - retro_nleu_872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.63 %
• Parental protein coverage: 63.01 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPSPHANRKKHRRKKSTSNFKADGLSGTAEEQEENFEFIIVSLTGQTWHFEATTYEERDAWVQAIESQIL
          P.SPH.NRKKHRR.K.TSNFKADGLSGTAEEQ.ENFEFIIVSLTGQTWHFEATT.EERD.WVQAIESQIL
Retrocopy PTSPHTNRKKHRRQKTTSNFKADGLSGTAEEQ-ENFEFIIVSLTGQTWHFEATTNEERDTWVQAIESQIL

Parental  ASLQSCESSKNKSRLTSQSEAMALQSIRNMRGNSHCVDCETQNPNWASLNLGALMCIECSGIHRNLGTHL
          ASLQSC.SSKNKS.L..QSEAMALQSI....GNSHCVD.ETQNPNWASLNLGALMCI.C.GIH.NLGTHL
Retrocopy ASLQSCKSSKNKSQLMNQSEAMALQSI*YTHGNSHCVDFETQNPNWASLNLGALMCI*CLGIHWNLGTHL

Parental  SR-VRSLDLDDWPVELIKVMSSIGNELANSVWEESSQGRTKPSVDSTREEKERWIRAKYEQKLFLAPLPC
          S..V.SLD.DDWPVELIK.MS.IGNEL.NSVWEESSQG.TKP.VDSTREEKE.WI.AKYEQKLFLAPLPC
Retrocopy SL>V*SLDQDDWPVELIKMMSPIGNELLNSVWEESSQGQTKPLVDSTREEKEQWIHAKYEQKLFLAPLPC

Parental  TELSLGQHLLRATADEDLRTAILLLAHGSRDEVNETCGEG--DGRTALHLACRKGNVVLAQLLIWYGVDV
          T.LSLGQHLLRATADEDL.TAILLL.HGSRDE..ET..EG..DG..ALHLAC.KGNVVL.QLLIWYGVDV
Retrocopy TDLSLGQHLLRATADEDLWTAILLLVHGSRDEAKETFREGD*DGCPALHLACHKGNVVLVQLLIWYGVDV

Parental  MARDAHGNTALAYARQASSQECIDVLLQYGCPDERFVLMATPNLSRRNNNRNNSSGRVPTIM
          MA.D.HGNT.LAY..QAS.QECI.VLL.YGCPDER.VLMA.PNLSRRNNNRN.SS.RVPTI.
Retrocopy MA*DTHGNTVLAYTWQASRQECINVLLEYGCPDER*VLMAIPNLSRRNNNRNSSSRRVPTII

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_872 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000010626	1 retrocopy	retro_nleu_872 ,