RetrogeneDB ID: retro_nleu_1876

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397313.1:11949257..11950189(-)
• Located in intron of: ENSNLEG00000005146

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L4
• Ensembl ID: ENSNLEG00000010841
• Aliases: None
• Description: None

Sequence

>retro_nleu_1876
CTAAAAAGAAGAATTAATGCATTGAAACCAATTCAGGTGAGATGCGCTCATATAGGAGCCAAGTTATTTGAAGAAGTTCA
TGACTTGGAAAGAAAATATGCAGCATTATACCAGCCTCTCTTTGACAAGAGAAGAGAATTTATCACCGGTGATGTTGAAC
CAACATCTGATATGGAATCAGAATGGCACAGTGAAAATGAAGAGGAGGAGAAATTGGCTGGAGACATGAAAAATAAAGTA
GTCATAACAGAAAAAGCAGCAGCAACAGCTGAATAGCCAAATCCCAAAGGAATTCCAGAGTTCTGGTTTACCATATTTAG
AAATGTAGATATGCTAAGTGAATTAGTCCAGGAATATGATGAACCAATCTTGAAACACCTGCAGGATATTAAAGTGAAGT
TTTCTGACCCTGGACAGCCTATGTCTTTTATATTAAGAGTTTCACTTTGAACCCAACGACTACTTTGCCAACTCAGTCCT
GAGAAAAAACCTGCAAGATGAAATCAGAACCAGATAAGGCTGATCCCTTTTTATTTGCAGGTCCTGAGATCATGGACTGC
GACGGGTATACTATTGACTGGAAGAAAGGAAAGAATGTTACTGTCAAAACCATCAAGAAAAAGCAGAAGCGTAAGGGTCC
AGGCACTGTTAGAACAATTACCAAACAAGTATCCAATGAGTCATTTTTCAACTTCTTCAATCCACTGAAAGCATCTGGGG
ATAGAGAATCACTGGATAAAGATTCCGAATTCGTATTAGCCTCTGATTTTGAAATTGGACACTTTTTCTGTGAGCGGATA
GTCCCGCAGGCTGTGCTGTACTTTGCTGGAGAGGCCTTAGAGGATGACGACAATTTTGACGAAGATGAAGAAGAGGGCGA
ATTAGAAGGTAACGAGGAGGGAGAAGATGAGGATGAGGTAGAAATTAATCCC

Alignment

ORF - retro_nleu_1876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.9 %
• Parental protein coverage: 82.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKRRINALKQLQVRCAHIEAKFYEEVHDLERKYAALYQPLFDKRREFITGDVEPT-DAESEWHSENEEEE
          .KRRINALK..QVRCAHI.AK..EEVHDLERKYAALYQPLFDKRREFITGDVEPT.D.ESEWHSENEEEE
Retrocopy LKRRINALKPIQVRCAHIGAKLFEEVHDLERKYAALYQPLFDKRREFITGDVEPTSDMESEWHSENEEEE

Parental  KLAGDMKNKVVITEKEAATAEEPNPKGIPEFWFTIFRNVDMLSELVQEYDEPILKHLQDIKVKFSDPGQP
          KLAGDMKNKVVITEK.AATAE.PNPKGIPEFWFTIFRNVDMLSELVQEYDEPILKHLQDIKVKFSDPGQP
Retrocopy KLAGDMKNKVVITEKAAATAE*PNPKGIPEFWFTIFRNVDMLSELVQEYDEPILKHLQDIKVKFSDPGQP

Parental  MSFVL-EFHFEPNDYFTNSVLTK-TYKMKSEPDKADPFSFEGPEIVDCDGCTIDWKKGKNVTVKTIKKKQ
          MSF.L.EFHFEPNDYF.NSVL.K.T.KMKSEPDKADPF.F.GPEI.DCDG.TIDWKKGKNVTVKTIKKKQ
Retrocopy MSFIL>EFHFEPNDYFANSVLRK>TCKMKSEPDKADPFLFAGPEIMDCDGYTIDWKKGKNVTVKTIKKKQ

Parental  KHKGRGTVRTITKQVPNESFFNFFNPLKASGDGESLDEDSEFTLASDFEIGHFFRERIVPRAVLYFTGEA
          K.KG.GTVRTITKQV.NESFFNFFNPLKASGD.ESLD.DSEF.LASDFEIGHFF.ERIVP.AVLYF.GEA
Retrocopy KRKGPGTVRTITKQVSNESFFNFFNPLKASGDRESLDKDSEFVLASDFEIGHFFCERIVPQAVLYFAGEA

Parental  IEDDDNFEEGEEGEEEELEGDEEGEDEDDAEINP
          .EDDDNF.E.E..EE.ELEG.EEGEDED..EINP
Retrocopy LEDDDNFDEDE--EEGELEGNEEGEDEDEVEINP

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_1876 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000205531	1 retrocopy	retro_hsap_438,
Gorilla gorilla	ENSGGOG00000013223	1 retrocopy	retro_ggor_423,
Nomascus leucogenys	ENSNLEG00000004682	4 retrocopies	retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Nomascus leucogenys	ENSNLEG00000010841	1 retrocopy	retro_nleu_1876 ,
Oryctolagus cuniculus	ENSOCUG00000005624	1 retrocopy	retro_ocun_384,
Pongo abelii	ENSPPYG00000002938	1 retrocopy	retro_pabe_288,
Pan troglodytes	ENSPTRG00000028747	1 retrocopy	retro_ptro_192,