RetrogeneDB ID: retro_nleu_2814

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397437.1:1372850..1373687(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPAL1
• Ensembl ID: ENSNLEG00000017377
• Aliases: None
• Description: None

Sequence

>retro_nleu_2814
GCTGCACATTTTGCTGCTTATGCTTTTGCAGCTGCCATCTTGGTCACCCTCACCCCCCCAGCCCTCTGAGTGTTCTCATA
AGTGCAATATTATTTTCCTATTTTTTAAATGAGCACTTGAACATTTATGGGAAAACAGGCTGCATATTGGGGTCAACTGT
GATGGTTATCCATGCCCCAGAAGAAGAGGAAGTCACTTCTTTGCATGAAATGGAAATGAAATTGAGAGACCCAGGATTTA
TTTCCTTTGCTGCGATCATAATTGTGATCTTGTTAGTGCTGATTTTGATTGTGGCTCCCAAGAAAGGACAGACCGATATA
TTGGTCTATATTTCAATCTGTTCTTTGACTGGAGCATTTTCAGTTTCTTCTGCCAAAGGCCTGGGTATTGCCATTAAGGA
ATTACTAGAGTGGAAGCCAGTTTGGAAGCATCCCCTGGTCATTTTTTGCTGGCTATACTTGTGTTTTTGGTGACTACACA
GATTAACCATCTCAAGGCACCAGACACCGTTAATACATCTCCTGTGACTCCCATTTATTCTGCGTTCTTCACATCCATGG
TAGTGACTTGCTCTGCCATCTTACTCCAAGAGTGGTATGGCATGAAAGCTGGAGATATCATCGAGACCCTGAGTGGATTC
TTCACTATTATCCTTGGCATCTTTCTTCTACATGCTTTTAAAAATACTGACATTACCTGGAGTAAGCTGACATCCACTGC
TAAGAAAGAAGTCATCTCTCTGAATGGCAATGAGAGCAATCCTGTTTTATTAGAGAACTTGGAGTGTTCAGCCCTGGATA
CAATGATAACGTTACCTTGTTTAGCAGAACTGATAAT

Alignment

ORF - retro_nleu_2814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.44 %
• Parental protein coverage: 68.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AANFAA--YAFAPATLVTPLGA-LSVLISAILSSYFLNEHLNIHGKIGCILSILGSTVMVIHSPKEEEVT
          AA.FAA...A.A.....TP....LSVLISAIL.SYFLNEHLNI.GK.GC...ILGSTVMVIH.P.EEEVT
Retrocopy AAHFAAYAFAAAILVTLTPPAL<LSVLISAILFSYFLNEHLNIYGKTGC---ILGSTVMVIHAPEEEEVT

Parental  SLHEMEMKLRDPGFISFAVIITVISLVLILIVAPKKGQTNILVYISICSLIGAFSVSSVKGLGIAIKELI
          SLHEMEMKLRDPGFISFA.II.VI.LVLILIVAPKKGQT.ILVYISICSL.GAFSVSS.KGLGIAIKEL.
Retrocopy SLHEMEMKLRDPGFISFAAIIIVILLVLILIVAPKKGQTDILVYISICSLTGAFSVSSAKGLGIAIKELL

Parental  AWKPVYKHPLVF-VLLAVLVLSVTTQINYLNKALDTFNTSLVTPIYYVFFTSMVVTCSAVLFQEWYGMTA
          .WKPV.KHPLV...LLA.LV..VTTQIN.L.KA.DT.NTS.VTPIY..FFTSMVVTCSA.L.QEWYGM.A
Retrocopy EWKPVWKHPLVI<FLLAILVFLVTTQINHL-KAPDTVNTSPVTPIYSAFFTSMVVTCSAILLQEWYGMKA

Parental  GDIIGTLSGFFTIIIGIFLLHAFKNTDITWSELTSTAKKEAVSLNVSENNYVLLENLECSA-PGYNDDVT
          GDII.TLSGFFTII.GIFLLHAFKNTDITWS.LTSTAKKE..SLN..E.N.VLLENLECSA.PGYND.VT
Retrocopy GDIIETLSGFFTIILGIFLLHAFKNTDITWSKLTSTAKKEVISLNGNESNPVLLENLECSA<PGYNDNVT

Parental  LFSRTDD
          LFSRTD.
Retrocopy LFSRTDN

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_2814 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002047	1 retrocopy	retro_dnov_2048,
Homo sapiens	ENSG00000163293	1 retrocopy	retro_hsap_2463,
Gorilla gorilla	ENSGGOG00000009006	1 retrocopy	retro_ggor_1533,
Macaca mulatta	ENSMMUG00000018625	1 retrocopy	retro_mmul_638,
Nomascus leucogenys	ENSNLEG00000017377	1 retrocopy	retro_nleu_2814 ,
Pongo abelii	ENSPPYG00000014714	1 retrocopy	retro_pabe_1810,
Pan troglodytes	ENSPTRG00000016038	1 retrocopy	retro_ptro_1422,