RetrogeneDB ID: retro_nleu_143

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: ADFV01137915.1:10957..11670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRAM1
• Ensembl ID: ENSNLEG00000006362
• Aliases: None
• Description: DNA-damage regulated autophagy modulator 1 [Source:HGNC Symbol;Acc:25645]

Sequence

>retro_nleu_143
ATGCTGTGCTTCCTGAGGGGAATGGCTTTCGTCCCCTGCCTCTTGGTGACCTGGTCGTCAGCAGCCTTCATTATCTCCTA
CATGGTCGCCGTGCTGTCCGGGCACGTCAACCCCTTCCTCCCCTACATCCGTGATACAGGAACACCACCTCCAGAAAGTG
GTATTTTTGGATTGATGATAAACTTCTCTGCATTTCTTGGTGCAGCCACGGTGTACACAAGATATAAAATCGTAGAGAAG
CAAAATCAAACCTGCTATTTCAGCACTCCTGTTTTTAACTTGGTGTCTTTAGTGCTTGGATTGGTGGCATGTTTCGGAAT
GTGCCTTGCCGCCGATTTTGAGGAGTTAGCTGTGCCAGTGGTTCATGACGCGGGCGCTCTTTTGGCCTTTGTCTGTGGTG
TCGTGTACACGCTTCTACAGTCCATCCTATCTTACAAGTAATATCCCGAGTGGAACAGTCTCTCGACATGCCACATACGG
ATGTTCATCGCTGCCGTTTCTTGCGCAGCTGTCATCCCCATGATTGTCTGTGCTTCACGAATTTCCATAACCAAGCTGGA
GTGGAATATAAGAGAAAAGGATTGTGTATATCACCTAGTGAGTGCGATCTGTGAATGGACAGTGGCCTTGGTTTTATTTT
CTACTTCCAAAATTTCATCCAAGATTTCCAGAGCGTCACCCAAAGGGTATCCGCAGAAATCAATGAGGATATT

Alignment

ORF - retro_nleu_143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.75 %
• Parental protein coverage: 96.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLRFLKGMAFLPFLLVTWSSAAFIISYVVAVLSRHVNPFLPYISDTGATPPESGIFGFMITFSAFLGAAT
          ML.FL.GMAF.P.LLVTWSSAAFIISY.VAVLS.HVNPFLPYI.DTG..PPESGIFG.MI.FSAFLGAAT
Retrocopy MLCFLRGMAFVPCLLVTWSSAAFIISYMVAVLSGHVNPFLPYIRDTGTPPPESGIFGLMINFSAFLGAAT

Parental  IYTRYKIIEKQNQTCYFSTPVFNLVSLVLGLVGCFGMGIVASFQELAVPVVHDGGALLAFVFGVLYTLLQ
          .YTRYKI.EKQNQTCYFSTPVFNLVSLVLGLV.CFGM...A.F.ELAVPVVHD.GALLAFV.GV.YTLLQ
Retrocopy VYTRYKIVEKQNQTCYFSTPVFNLVSLVLGLVACFGMCLAADFEELAVPVVHDAGALLAFVCGVVYTLLQ

Parental  SIISYKSCPQWNSLSTCRIRMFISAVACAAVIPMIVCASLISITKLEWNPRDKDYIYHIVSAICEWTVA-
          SI.SYK..P.WNSLSTC.IRMFI.AV.CAAVIPMIVCAS.ISITKLEWN.R.KD..YH.VSAICEWTVA.
Retrocopy SILSYK*YPEWNSLSTCHIRMFIAAVSCAAVIPMIVCASRISITKLEWNIREKDCVYHLVSAICEWTVA<

Parental  FGFIFYFLTFIKDFQSITLRISAETNGDV
          .GFIFYF..FI.DFQS.T.R.SAE.N.D.
Retrocopy LGFIFYFQNFIQDFQSVTQRVSAEINEDI

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_143 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027549	1 retrocopy	retro_cpor_1427,
Nomascus leucogenys	ENSNLEG00000006362	2 retrocopies	retro_nleu_143 , retro_nleu_2841,
Tursiops truncatus	ENSTTRG00000017217	1 retrocopy	retro_ttru_189,