RetrogeneDB ID: retro_nleu_1323

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397289.1:2346541..2347093(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPRD1A
• Ensembl ID: ENSNLEG00000006228
• Aliases: None
• Description: None

Sequence

>retro_nleu_1323
GCTCTGTGTGGTGATAAGAAGCCTAGGAAGCAAATTTATAAACAGATAAAGATGAATGAAAATAAAAACTGTTCCTCTCT
GGGATCTGCAAATGAGCCACCATCACAGACTCTAAATCTCATGACAGCATTACAAAATCTAGAAAATGCAGCCTTGGGTG
ATGCAGCAGTTCACTAGAGGATCGCTTTTTTGCCTGCTGTAGACCAAGAAGTATCTCTACTAGATAAAATAGCAGATAAA
GAACCCGGAGAAAGACTTTCTAAAATGATGGATGCGTGTATGTTGCCGGCAGATTACAATGGCAGAATGGCAGCAGAAAT
AGATGAGAGGAAGCAACTCACTCGAATGTTAGCAGATTTTCTTCATTGTCCAATGGAAGCCCTTGCAGAGAAAGCATAAA
TTGGAAGAATACAAGTGCAAGTGAGCCAGAGTTTCCCTGGTGTGCAAAGAATTCAGGTTCCCGATCCAGAGCCTGTCAGA
CTAATCTTGATTACCCAATGTCACTGGCAGCCACATGCACCTGCCCTTTGCAGGGACATCTACAGTGAAGAT

Alignment

ORF - retro_nleu_1323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.47 %
• Parental protein coverage: 59.29 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALYGDKKPRKRTYEQIKVDENENCSSLGSPSEPP-QTLDLVRALQDLENAASGDAAVHQRIASLPVEVQE
          AL.GDKKPRK..Y.QIK..EN.NCSSLGS..EPP.QTL.L..ALQ.LENAA.GDAAVH.RIA.LP...QE
Retrocopy ALCGDKKPRKQIYKQIKMNENKNCSSLGSANEPPSQTLNLMTALQNLENAALGDAAVH*RIAFLPAVDQE

Parental  VSLLDKITDKESGERLSKMVEDACMLLADYNGRLAAEIDDRKQLTRMLAD-FLRCQKEALAEKEHKLEEY
          VSLLDKI.DKE.GERLSKM..DACML.ADYNGR.AAEID.RKQLTRMLAD.F...Q...L....HKLEEY
Retrocopy VSLLDKIADKEPGERLSKMM-DACMLPADYNGRMAAEIDERKQLTRMLAD>FFIVQWKPL-QRKHKLEEY

Parental  KRKLARVSLVRKELRSRIQSLPDLSRLPNVTGSHMHLPFAG-DIYSED
          K.K.ARVSLV.KE.R..IQSL.D.S.LPNVTGSHMHLPFAG.DIYSED
Retrocopy KCK*ARVSLVCKEFRFPIQSLSD*S*LPNVTGSHMHLPFAG<DIYSED

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_1323 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007025	1 retrocopy	retro_eeur_245,
Gorilla gorilla	ENSGGOG00000007369	1 retrocopy	retro_ggor_1237,
Macaca mulatta	ENSMMUG00000018777	1 retrocopy	retro_mmul_1562,
Monodelphis domestica	ENSMODG00000000399	1 retrocopy	retro_mdom_360,
Nomascus leucogenys	ENSNLEG00000006228	1 retrocopy	retro_nleu_1323 ,
Pongo abelii	ENSPPYG00000009111	1 retrocopy	retro_pabe_1352,
Pan troglodytes	ENSPTRG00000009974	1 retrocopy	retro_ptro_1106,
Vicugna pacos	ENSVPAG00000001641	1 retrocopy	retro_vpac_62,