RetrogeneDB ID: retro_nleu_2992

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397556.1:174870..175753(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOA1BP
• Ensembl ID: ENSNLEG00000012663
• Aliases: None
• Description: None

Sequence

>retro_nleu_2992
GCGTCGCGCTGGGCCAGGGGCGCGCGCTCTGCGAGCAGGATGTCCGGCCTGCGGGCGCTGCTGGTTGCGGCTCGCGCCTG
CCGCGAATCAAAAGCCAGACCAGCACCTGCCGCTCAGGACCCACCTAGTGGGGACCGCAGCGGCTAAACTCGAGTGGCCG
CTGGGATTCAGCGGTCATAGCGAGCATAGCGGTGAAGCACCTGAGCCAGAAGGAAGCCCAGGCCGTGGCCGGGAGCTATT
GAACGAATACCAGTTCAGCGTGGACCCACTTATGGAGCTGGCCGGGCTGAGCTGTGCCACAGCCATCGCAAAGGCATATC
CCCCCACGTCCATGTCCAGGAGCCCCCCTACTGTCCTGGTCACCTGTGGCCCGGGGAATAATGGAGGAGATGGTCTGGTC
TGTGCTCCACGTCTCAAACTCTTTGGCTAACCAGCCAACCACCTATTACCCCAAAAGGCCTAACAAGCCCCTCTTCATTG
CGTTGGTGACCCAGTGTCAGAAAATGGACATCCCTTTCCTTGGGGAAATGAGCTCAGAGCCTGTCATGATTGAGCTGTAT
GAGCTGGTGGTGGATGCCATCTTCGGCTTCAGCTTCGAGGGCGATGTTCGGGAACCGTTCCACAGCATCCTGAGTGTCCT
GGAGGGACTCACTGTGCCCATTGCCGGCATCCACATTCCCTCAGGATGGGATGTGGAGAAGGGAAACTCTGGAGGGATCC
AGCCAGACTTGCTCATCTCCCTCACAGCACCCAAAAAGTCTGCAACCCAGGCTACCGGTCGCCACCATTACCTGGGGGGT
CGTTTTGTGCCACCTGCTCTGGAAAAGAAGTAGCAGCTGAACCTGCCCCCTACCCTGACACCAAGTGTGTCTATGGTCTG
CAG

Alignment

ORF - retro_nleu_2992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83. %
• Parental protein coverage: 97.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SASWMSGLRA---LLGL-GLLVA-GSRLPRIKSQTIACRSGPTWWGPQRLNSGGRWESEVMASTAVKYLS
          ...W..G.R......GL..LLVA.GSRLPRIKSQT..CRSGPT.WGPQRLNS.GRW.S.V.AS.AVK.LS
Retrocopy ASRWARGARSASRMSGLRALLVA<GSRLPRIKSQTSTCRSGPT*WGPQRLNSSGRWDSAVIASIAVKHLS

Parental  QEEAQAV-DQELFNEYQFSVDQLMELAGLSCATAIAKAYPPTSMSRSPPTVLVICGPGNNGGDGLVCARH
          Q.EAQAV...EL.NEYQFSVD.LMELAGLSCATAIAKAYPPTSMSRSPPTVLV.CGPGNNGGDGLVCA..
Retrocopy QKEAQAV<GRELLNEYQFSVDPLMELAGLSCATAIAKAYPPTSMSRSPPTVLVTCGPGNNGGDGLVCAPR

Parental  LKLFG-YEPTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPSEPMMIDELYELVVDAIFGFSFKGDVREP
          LKLFG...PT.YYPKRPNKPLF.ALVTQCQKMDIPFLGEM.SEP.MI.ELYELVVDAIFGFSF.GDVREP
Retrocopy LKLFG>NQPTTYYPKRPNKPLFIALVTQCQKMDIPFLGEMSSEPVMI-ELYELVVDAIFGFSFEGDVREP

Parental  FHSILSVLKGLTVPIASIDIPSGWDVEKGNSGGIQPDLLISLTAPKKSATQFTGRYHYLGGRFVPPALEK
          FHSILSVL.GLTVPIA.I.IPSGWDVEKGNSGGIQPDLLISLTAPKKSATQ.TGR.HYLGGRFVPPALEK
Retrocopy FHSILSVLEGLTVPIAGIHIPSGWDVEKGNSGGIQPDLLISLTAPKKSATQATGRHHYLGGRFVPPALEK

Parental  KYQLNLP-PYPDTECVYRLQ
          K.QLNLP.PYPDT.CVY.LQ
Retrocopy K*QLNLP<PYPDTKCVYGLQ

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_2992 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000163382	2 retrocopies	retro_hsap_1973, retro_hsap_3275,
Gorilla gorilla	ENSGGOG00000000754	1 retrocopy	retro_ggor_2228,
Macaca mulatta	ENSMMUG00000002623	2 retrocopies	retro_mmul_1364, retro_mmul_2060,
Nomascus leucogenys	ENSNLEG00000012663	2 retrocopies	retro_nleu_2615, retro_nleu_2992 ,
Pongo abelii	ENSPPYG00000000713	2 retrocopies	retro_pabe_1692, retro_pabe_2709,
Pan troglodytes	ENSPTRG00000001463	2 retrocopies	retro_ptro_1315, retro_ptro_2215,