RetrogeneDB ID: retro_nleu_2615

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397382.1:3285222..3285839(+)
• 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_2615
AGCATGGCCCAACTTACAGAATTGGCTGGGCTCAGCTGTTCCACTGTCATTGCCAAGGCATATCCTCCCATATCCATGTC
CAGGGCCCCTGCTACTGTTCCGATCATCCATGGCCCAGGGAATAATGGAGAAGGTAGCCTGCTCTGTGCTTGACACTCCA
AACATTTTGGTCACCAGCCAATCATCTTTGACCCCAAAAGACCCAACAAGCCACTCTACACTATGCTGGTGACCCATCGT
CAGGAAAGGGACATTCTCTTGCTTGGTGAAGTGCCCCCAGAGCCCATGCTGATCAATGAGCTGTATGGGCTGGGGGTGGA
TGCCATCTTTGCTTCAGCTTCAAGGGCAATGTTTGAAAGCCATTCTGTAACATTCTGAGTGTCCTGAATGGACTCACTGT
GCCACTGCCAATGCTGACATTCCCTTGGAATGGGATTTGGAGAAGGAAAACTCTGGAGGGATCCAGCCAGAACTGCTTCT
CTCCCTGATAGCACCCAAAAAGTCTGAAACCTAGTTTACAGATTGCTACCACTACTTGAGGGGTTGTTGACTGCCACCTG
CTTTGGAAAAGAAGTACCAGCTAAAACCTACCATTGTACCCTAACCCTGAGTATGTC

Alignment

ORF - retro_nleu_2615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.99 %
• Parental protein coverage: 68.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVDQLMELAGLSCATAIAKAYPPTSMSRSPPTVLVICGPGNNGGDGLVCARHLKLFGYEPTIYYPKRPNK
          S..QL.ELAGLSC.T.IAKAYPP.SMSR.P.TV..I.GPGNNG...L.CA.H.K.FG..P.I..PKRPNK
Retrocopy SMAQLTELAGLSCSTVIAKAYPPISMSRAPATVPIIHGPGNNGEGSLLCA*HSKHFGHQPIIFDPKRPNK

Parental  PLFTALVTQCQKMDIPFLGEMPSEPMMIDELYELVVDAIFG-FSFKGDVREPFHSILSVLKGLTVPI-AS
          PL.T.LVT..Q..DI..LGE.P.EPM.I.ELY.L.VDAIF..FSFKG.V..PF..ILSVL.GLTVP..A.
Retrocopy PLYTMLVTHRQERDILLLGEVPPEPMLINELYGLGVDAIFA<FSFKGNV*KPFCNILSVLNGLTVPL<AN

Parental  IDIPSGWDVEKGNSGGIQPDLLISLTAPKKSATQFTGRYHYLGGRFVPPALEKKYQL-NLPPYPDTECV
          .DIP..WD.EK.NSGGIQP.LL.SL.APKKS.T.FT..YHYL.G...PPALEKKYQL.NLP.YP..E.V
Retrocopy ADIPLEWDLEKENSGGIQPELLLSLIAPKKSET*FTDCYHYLRGC*LPPALEKKYQL>NLPLYPNPEYV

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_2615 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,