RetrogeneDB ID: retro_nleu_2424

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397354.1:1645815..1646552(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTGR1
• Ensembl ID: ENSNLEG00000017487
• Aliases: None
• Description: None

Sequence

>retro_nleu_2424
ATGATTCATGCTAAGAGATGGACCCTGAAGAAGCACTTTGTTGGCAATCCTACTAGTAGTGACTTTGAGTTGAAGACAGC
TGAGCTCCCACCCTTAAAAAATAGAGAGGTCCTGCTTGAAGCTTTGTTCCTCACTGGGGACCCTTACATGAGAGTGGCAG
CCAAAAGACTGAAGGAAGGTGATACAATGATGGGGCAGCAAGTGGCCAGATTTGTGGAAAGTAAAAATGCAGCCTTACCA
ACAGGAACTATTGTACTGGCTCCTTCAGGCTGGACAGCACACTCCATTTCTGATGGAAAAGATCTGGAAAAGCTGCCAAC
AGAGTGGCCTGACACAGTACCACTGTCTCTGGCTCTGGGGACAGTTAGCATGACAGGCCTCACTGCCTACTTTGGCCTAC
TTGACATCTGTGGTGTGAAGGGTGGAGAAACAGTGATGGTTAATGCAGCAGCTGGAGCTGTGGGCTCTGTTTTGGGGCAG
ATTACAAAGTTCAAGGGCTGCAAAGTGGTTGGAGCAGTAGGGTCTGACAAAAAGACTGCCTACCTTAAAAAGCTTGGATC
TGATGTTGTCTTTAACTACAAGACAGTAGAGTCTTTGAAGAAATTTTGAAGAAATCCTCTCCTGATGGTTACAATTGTTA
TTTTGATAATGTAAGTGGATAGTTTTCAAACACTGTTATCTCCCAGATGAAGAAATTTGCAAGAATTGCCATATGTGGAG
CTATCTCTACATATAAC

Alignment

ORF - retro_nleu_2424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 74.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVRTKTWTLKKHFVGYPTNSDFELKTAELPPLKNGEVLLEALFLTVDPYMRLAAKRLKEGDTMMGQQVAK
          M...K.WTLKKHFVG.PT.SDFELKTAELPPLKN.EVLLEALFLT.DPYMR.AAKRLKEGDTMMGQQVA.
Retrocopy MIHAKRWTLKKHFVGNPTSSDFELKTAELPPLKNREVLLEALFLTGDPYMRVAAKRLKEGDTMMGQQVAR

Parental  VVESKNAALPKGTIVLASSGWTTYSISDGKDLEKLLTEWPDTIPLSLALGTVGMPGLTAYFGLLEICGVK
          .VESKNAALP.GTIVLA.SGWT..SISDGKDLEKL.TEWPDT.PLSLALGTV.M.GLTAYFGLL.ICGVK
Retrocopy FVESKNAALPTGTIVLAPSGWTAHSISDGKDLEKLPTEWPDTVPLSLALGTVSMTGLTAYFGLLDICGVK

Parental  GGETVMVNAAAGAVGSVVGQIAKLKGCKVVGAVGSDEKVAYLQKLGFDVVFNYKTVESL-EETLKKASPD
          GGETVMVNAAAGAVGSV.GQI.K.KGCKVVGAVGSD.K.AYL.KLG.DVVFNYKTVESL.EE.LKK.SPD
Retrocopy GGETVMVNAAAGAVGSVLGQITKFKGCKVVGAVGSDKKTAYLKKLGSDVVFNYKTVESL<EEILKKSSPD

Parental  GYDCYFDNVGGEFSNTVISQMKKFGRIAICGAISTYN
          GY.CYFDNV.G.FSNTVISQMKKF.RIAICGAISTYN
Retrocopy GYNCYFDNVSG*FSNTVISQMKKFARIAICGAISTYN

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_2424 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003000	2 retrocopies	retro_cfam_1290, retro_cfam_1876,
Callithrix jacchus	ENSCJAG00000017571	1 retrocopy	retro_cjac_1653,
Echinops telfairi	ENSETEG00000006136	1 retrocopy	retro_etel_358,
Felis catus	ENSFCAG00000004339	1 retrocopy	retro_fcat_1898,
Homo sapiens	ENSG00000106853	1 retrocopy	retro_hsap_219,
Nomascus leucogenys	ENSNLEG00000017487	1 retrocopy	retro_nleu_2424 ,
Otolemur garnettii	ENSOGAG00000011144	1 retrocopy	retro_ogar_2834,
Pongo abelii	ENSPPYG00000019499	1 retrocopy	retro_pabe_283,