RetrogeneDB ID: retro_nleu_1985

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397321.1:602217..603346(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UHRF2
• Ensembl ID: ENSNLEG00000009135
• Aliases: None
• Description: None

Sequence

>retro_nleu_1985
TCTGAAGGAGCATTAAATGAGTGCAAGATAATATCTGTAGATGAAATCTTCAAGACCGAGAAACCTGGAGCCCATCCTCT
TTCATTTGCAGATGTAAAGTTTTTAAGGAGAAATAACCCTGAATGTGACCTGTGTGGTGGAGACCCAGATAAGAAATGCC
ATTCTTGCTTCTTTCATGTATATGGTGGGAAACATGAACCCAACATGCAGCTTCTATGTGATGAATGTAATGTGGCTTAT
CATATTTACTGCTTGAATACACCTTTGGATAACGTCCCAGAAGAGGAATACTGGTATTGTTCTTCCTGTAAAACTGATTC
CAGTTAAGTTGTAAAGGCTGGTGAAAGACTCGAGATGAGCAAAAAGAAAGCAAAGATGCCATCCGCTAGTACTGAAAGCC
AGAGAGACTGGTGCAGGACAATGGCTTGTGTTGGTCATATGATAGAATGTACTATTGTCTCTTCTAATCATTATGGACCT
ATTCCTGTTGGATCAACTTGGAGATTTAGAGTTCAGGTGAGTCAAAGTAGGTGTTCACAGACCCCATGTTGGCGGACTTC
ATGGTTGAAGTAATGATGGAGTTTATTCTCTTGTCTTGGCTGGTGGATTTGTGGATAAAGTTGACCGAGGTGATGAGTTC
TTATACACTGGAAGTGGTGGTAAAAAGCTTGCTGGTAATAAAAGAATTGGCACATCTTCAGCTGATCAAACATTAACAAA
CACGAACAGGGCATTGGCCCTAAACTGTGATGCTACATCGGGTGATAAAATTGGAGCAGAGTCTCGGAATTAGAGAGCTG
GTAAGCCAGTCAGAGTGATATGCAGTTTTAAAGGGAAGAAGACCAGCAAATATGCTCCTGAAGAAGGCAACAGATATGAT
GGCATTTATAAGGTAGTGAAATACTGGCCAGAGATTTCATCAAGCCATGGATTCTTGATTTGGTGCTATCTTTTAAGAAG
AGATGATGTTGAACCTGCTTCTTGGACCTCTGAAGGAATAGAATGGTCAAGGACATTATGTCTACATTTACAGTATCCAG
CAGGTTACCCTTCAGATAAAGAAAGGAAGAAGACTAAAGGACAGTCAAGGAAGCAGGTCAGTGGAATCACAGAAAGGCCG
ATTTCAGAT

Alignment

ORF - retro_nleu_1985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.74 %
• Parental protein coverage: 50.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEGTLNDCKIISVDEIFKIERPGAHPLSFADGKFLRRNDPECDLCGGDPEKKCHSCSCRVCGGKHEPNMQ
          SEG.LN.CKIISVDEIFK.E.PGAHPLSFAD.KFLRRN.PECDLCGGDP.KKCHSC...V.GGKHEPNMQ
Retrocopy SEGALNECKIISVDEIFKTEKPGAHPLSFADVKFLRRNNPECDLCGGDPDKKCHSCFFHVYGGKHEPNMQ

Parental  LLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKTDSSEVVKAGERLKMSKKKAKMPSASTESRRDWGRG
          LLCDECNVAYHIYCLN.PLD.VPEEEYWYC.SCKTDSS.VVKAGERL.MSKKKAKMPSASTES.RDW.R.
Retrocopy LLCDECNVAYHIYCLNTPLDNVPEEEYWYCSSCKTDSS*VVKAGERLEMSKKKAKMPSASTESQRDWCRT

Parental  MACVGRTRECTIVPSNHYGPIPGIPVGSTWRFRVQVSEA-GVHRPHVGGIHGRSNDGAYSLVLAGGFADE
          MACVG...ECTIV.SNHYGP...IPVGSTWRFRVQVS...GVHRPHVGG.HG.SNDG.YSLVLAGGF.D.
Retrocopy MACVGHMIECTIVSSNHYGP---IPVGSTWRFRVQVSQS>GVHRPHVGGLHG*SNDGVYSLVLAGGFVDK

Parental  VDRGDEFTYTGSGGKNLAGNKRIGAPSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSF
          VDRGDEF.YTGSGGK.LAGNKRIG..SADQTLTN.NRALALNCDA...DKIGAESRN.RAGKPVRVI.SF
Retrocopy VDRGDEFLYTGSGGKKLAGNKRIGTSSADQTLTNTNRALALNCDATSGDKIGAESRN*RAGKPVRVICSF

Parental  KGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYP
          KG.K.SKYAPEEGNRYDGIYKVVKYWPEISSSHGFL.W.YLLRRDDVEPA.WTSEGIE.SR.LCL.LQYP
Retrocopy KGKKTSKYAPEEGNRYDGIYKVVKYWPEISSSHGFLIWCYLLRRDDVEPASWTSEGIEWSRTLCLHLQYP

Parental  AGYPSDKEGKKTKGQSKKQPRGTTKRPISD
          AGYPSDKE.KKTKGQS.KQ..G.T.RPISD
Retrocopy AGYPSDKERKKTKGQSRKQVSGITERPISD

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_1985 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.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147854	1 retrocopy	retro_hsap_4708,
Gorilla gorilla	ENSGGOG00000008853	1 retrocopy	retro_ggor_2925,
Nomascus leucogenys	ENSNLEG00000009135	1 retrocopy	retro_nleu_1985 ,
Nomascus leucogenys	ENSNLEG00000013406	1 retrocopy	retro_nleu_1267,
Pongo abelii	ENSPPYG00000019227	1 retrocopy	retro_pabe_3656,