RetrogeneDB ID: retro_nleu_2013

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397323.1:1273835..1274317(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIR1
• Ensembl ID: ENSNLEG00000005869
• Aliases: None
• Description: None

Sequence

>retro_nleu_2013
ATGGGGAAATCCTTCACCAACTTCAAGTGCAAGAAGGACTTTCATCCCACCTCTAAATCTAATATCAAAAAAATATGGAG
GGAAGAATAGAAAATATCATATGGTAAGAAGAAATAAGAAGAATTAATGCAACAATATCTTTAAGAACAAGAATCGTACG
ATAACAGCTTGGTTATGGGATATGAATCTGTAAAGAATGGTCTTGATTTCATGTATGAAGCCCCACCAGGAGTTTAAAAA
GTAGACAAAGAGAAAGAAGAAACAGAGGAGAGACGGGATACAAATTTGAATGGCAGAAAGGAGCACTACAAGAAAAATAT
GCCAAAGATGACATGAACATCAGAGATCAACCCTTTGGTATTCAGGTTTGAAATGTGAGGGGCATTAAATGTCACAAATG
GGGTCATGTCAACACAGATCAAGAATACCCTTTGTTGGGTCTTTCCGGAATCAATGCAAGCTCAGTTCCCAGTGATGGTT
CA

Alignment

ORF - retro_nleu_2013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.1 %
• Parental protein coverage: 79.9 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKSFANFMCKKDFHPASKSNIKKVWMAEQKISYDKKKQEELMQQYLKEQESYDNRLLMGDERVKNGLNF
          MGKSF.NF.CKKDFHP.SKSNIKK.W..E.KISY.KKK.EELMQQYL.EQESYDN.L.MG.E.VKNGL.F
Retrocopy MGKSFTNFKCKKDFHPTSKSNIKKIWREE*KISYGKKK*EELMQQYL*EQESYDNSLVMGYESVKNGLDF

Parental  MYEAPPGAKKENKEKEETE-GETEYKFEWQKGAPREKYAKDDMNIRDQPFGIQAIVRNVRCIKCHKWGHV
          MYEAPPG..K..KEKEETE.GET.YKFEWQKGA..EKYAKDDMNIRDQPFGIQ..V.NVR.IKCHKWGHV
Retrocopy MYEAPPGV*KVDKEKEETE<GETGYKFEWQKGALQEKYAKDDMNIRDQPFGIQ--V*NVRGIKCHKWGHV

Parental  NTDRECPLFGLSGINASSVPTDGS
          NTD.E.PL.GLSGINASSVP.DGS
Retrocopy NTDQEYPLLGLSGINASSVPSDGS

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_2013 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007884	1 retrocopy	retro_cjac_2152,
Homo sapiens	ENSG00000138433	2 retrocopies	retro_hsap_3082, retro_hsap_3394,
Macaca mulatta	ENSMMUG00000023006	1 retrocopy	retro_mmul_1967,
Mustela putorius furo	ENSMPUG00000013943	1 retrocopy	retro_mputfur_178,
Mus musculus	ENSMUSG00000041777	2 retrocopies	retro_mmus_2064, retro_mmus_3104,
Nomascus leucogenys	ENSNLEG00000005869	3 retrocopies	retro_nleu_1540, retro_nleu_2013 , retro_nleu_2691,
Pan troglodytes	ENSPTRG00000012652	2 retrocopies	retro_ptro_2079, retro_ptro_2306,