RetrogeneDB ID: retro_nleu_2733

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397411.1:1075000..1075656(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF1
• Ensembl ID: ENSNLEG00000003587
• Aliases: None
• Description: None

Sequence

>retro_nleu_2733
AAAGGCCGCCCTCTGCATGAGGTCTTGCTGGAACAAGCCAAGGTTGTCTGACAGTTCTAGGGGAGAGAAGACTTGGATAA
GTAGATAGTGACTTCTGAAAAGACAATTGGAGGCAGAAGTGAAGTATTTTTGAAAATGGGCAAGAATAACCAAAGTGCAC
TGCTATATGGAACTCTGAGCTCTGAGGTGCCTCAGGATGGGGAGACTACCTGAAGTGAGTACTGTGCAATGATATCCAGG
ATTCCAGGGGGTGCTTTTGAGAGGAAGATGTCTTATGTTTGGTCCCAGTTCAGTACTCTGTATCTCCGTGTACGTGGGGA
TGGTTGGCCTTGGATGATGAATATCAGGGAGGACACAGATATAATCCAGAGGAAAATCAGATGTATAGCTACTTCATGTT
CACCCGTGGGGAGCCCTACTGGCAGAAGGTCAACATCCCTTTTTCCAATTTTTTTTTCCCTAATCAAGGAAGAGTGCAGG
ATGTTCAGAGTCAGCTTCTGCTTGACAAGACCTCTTCTATAGCATTCACCTTGGCTGATAAAGTGGATGGTCCATTCTTC
CTGGAGACAGATTTTATTGGAGTGCTTACTGATCCAGCCCACACAGAAGAATTTGCCTATGAAAGTTCTCCAGAGCTTAA
CCCAAGACTTTTAAAA

Alignment

ORF - retro_nleu_2733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.09 %
• Parental protein coverage: 68.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGRPLHDVLLEQAKVVWQFRGKEDLDKWTVTSDKTIGGRSEVFLKMGKNNQSALLYGTLSCEAPQDGEST
          .GRPLH.VLLEQAKVV.QF.G.EDLDK..VTS.KTIGGRSEVFLKMGKNNQSALLYGTLS.E.PQDGE.T
Retrocopy KGRPLHEVLLEQAKVV*QF*GREDLDK*IVTSEKTIGGRSEVFLKMGKNNQSALLYGTLSSEVPQDGETT

Parental  RSGYCAMISRIPRSAFERKMSYDWSQFNTLYLRVHGDGRPWMVNIKEDIDFFQRR-NQMYSYFMFTRGGP
          .S.YCAMISRIP..AFERKMSY.WSQF.TLYLRV.GDG.PWM.NI.ED.D..QR..NQMYSYFMFTRG.P
Retrocopy *SEYCAMISRIPGGAFERKMSYVWSQFSTLYLRVRGDGWPWMMNIREDTDIIQRK<NQMYSYFMFTRGEP

Parental  YWQEVKIPFSKFFFSNRGRIRDVQHELPLDKISSIGFTLADKVDGPFFLEIDFIGVFTDPAHTEEFAYEN
          YWQ.V.IPFS.....N.GR..DVQ..L.LDK.SSI.FTLADKVDGPFFLE.DFIGV.TDPAHTEEFAYE.
Retrocopy YWQKVNIPFSXXXXPNQGRVQDVQSQLLLDKTSSIAFTLADKVDGPFFLETDFIGVLTDPAHTEEFAYES

Parental  SPELNPRLVK
          SPELNPRL.K
Retrocopy SPELNPRLLK

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_2733 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000025980	1 retrocopy	retro_ggor_1492,
Microcebus murinus	ENSMICG00000016845	1 retrocopy	retro_mmur_637,
Nomascus leucogenys	ENSNLEG00000003587	1 retrocopy	retro_nleu_2733 ,
Pongo abelii	ENSPPYG00000006373	2 retrocopies	retro_pabe_1683, retro_pabe_1684,
Pan troglodytes	ENSPTRG00000006945	1 retrocopy	retro_ptro_1383,