RetrogeneDB ID: retro_nleu_3091

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397972.1:925..1777(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000016146
• Aliases: None
• Description: None

Sequence

>retro_nleu_3091
ACCCTCCCCGCGGAAGCCCAAGGACGAGGACGGCGAAGGAGACTCCCTTGGACCCAGAGCCAAAGCGAGGCCCTGCGAGC
CCGCTTTCAGCGGAACCCATACCTGGGCATCGCCACCAGAGAAGGGCTGGCCCAGGCCATAGGCATTCCGGAGCCCAGGG
TCCAGATTTGGTTTCAGAATGGGAGGTCACGTCAGCTGAGGCAGCACCGGCGGGAATCTCGGCCCTGGCCCTGGAGACGC
GGCCCGCAAGAAGACAGGAGAAAGCGGACCGATGTCACCGGATCCCAGACCGCCCTGCCGGTTCGAGCCTTTGAGAAGGA
TCGCTTTCCAGGCATCGCCACCAGGGAAGAACTGGCCAGAGAGACGGGCCTCCCAGAGTCCAGGATTCACATCTGGTTTC
AGAATCGAAGGGACAGGCACCCGGGACAGGGTGGCAGGGCGCCCGCGCACACAGGCGGTCTGTGCAACGCGGCCCCCGGC
GGGTATCACCCTGCTCCCTGGTCGGTCGCCTTCGCCCACACCGGGGCGTGGTGAACGGGGCTCCCCGCACCCCGCATGCC
CTGCGCGCCTGGGACTCTCCCACAGGGTGCTTTCTTGAGCCAGGGAGCAAGGGCCGTGCCCCTGCTCCAGCCCAGCCAGG
CTGTGCCGGCAGAAGGGATCTCCCAACCTGCCCCGGCAGGCGGGGATTTTGCCTACGCCGCCCTGGCTCCTCCGGAAGGG
GTGCTCTCCCACCCTCAGACTCCTCGGTGGCCTCCGCACCCGAGCCAATGCCGGGAGGACCGGGACCCGCAGCGCGACGG
CCTGCCGGGCCCTTGCGCGGTGGGACAGCCGGGGCCCGCTCAAGCTGGGCCA

Alignment

ORF - retro_nleu_3091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 60.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLPAEARGRGRRRRLVWTPSQSEALRACFERNPYPGIATRERLAQAIGAPEPRVQIWFQNERSRQLRQHR
          TLPAEA.GRGRRRRL.WT.SQSEALRA.F.RNPY.GIATRE.LAQAIG.PEPRVQIWFQN.RSRQLRQHR
Retrocopy TLPAEAQGRGRRRRLPWTQSQSEALRARFQRNPYLGIATREGLAQAIGIPEPRVQIWFQNGRSRQLRQHR

Parental  RESRPWPGRRGPPEGRRKRTSVAPSQTALLLRAFEKDRFPDIATRERLARETGLPESRIHVWFQNRRARH
          RESRPWP.RRGP.E.RRKRT.V..SQTAL..RAFEKDRFP.IATRE.LARETGLPESRIH.WFQNRR.RH
Retrocopy RESRPWPWRRGPQEDRRKRTDVTGSQTALPVRAFEKDRFPGIATREELARETGLPESRIHIWFQNRRDRH

Parental  PGQGGRAAAHAGGPCNAAPGRCHPAPWSVAPAGTSRRGRGLPSGFHPLAHGGLSQGSAAGKKGWSLPACG
          PGQGGRA.AH.GG.CNAAPG..HPAPWSVA.A.T.....GLP....P.A.G.L.QG..........P...
Retrocopy PGQGGRAPAHTGGLCNAAPGGYHPAPWSVAFAHTGAW*TGLPAPRMPCAPGTLPQGAFLSQGARAVPLLQ

Parental  PCNAAPGGCHPAPWSVAPAGGDVAYAALAPPEGALSHPQAPRWPPHPPSKCPGDRDPQRHGLPGLPAQAG
          P..A.P......P...APAGGD.AYAALAPPEG.LSHPQ.PRWPPH.PS.C..DRDPQR.GLPG.P...G
Retrocopy PSQAVPAEGISQP---APAGGDFAYAALAPPEGVLSHPQTPRWPPH-PSQCREDRDPQRDGLPG-PCAVG

Parental  PQGQGVLAP
          ..G.....P
Retrocopy QPGPAQAGP

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_3091 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006577	2 retrocopies	retro_chof_1700, retro_chof_2634,
Nomascus leucogenys	ENSNLEG00000010886	3 retrocopies	retro_nleu_1935, retro_nleu_2214, retro_nleu_568,
Nomascus leucogenys	ENSNLEG00000016146	2 retrocopies	retro_nleu_2945, retro_nleu_3091 ,