RetrogeneDB ID: retro_nleu_405

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:1435113..1435596(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000004194
• Aliases: None
• Description: None

Sequence

>retro_nleu_405
ATGCCCTTGAAGGGGCCCTCTGATGCCTGCTTCACCATTTCTTGATGTCATCATATTTGGCAGGTTTTTCCAGATGGCAG
GTCAGGTCCACTACCAACACATTGGTGGTGGGGACACGGAAGGCTTTGCCAGTGAGCTTCCTGTTCAGCTCAGGGATGAC
CTTGTCTACAGCCTTGGCAGCACCAGGAGAGGCAGGGATGATGTTCTGGAGAGCCCTGCGGCCATCACACCAGTTTCCCA
GAGGGGCTATCCACAGTCTTCTGGGTGGCAGCAATGGCATGGACTGTGGTCATGAGTCCTTCCATGATACCAAAGTTGTC
ATGGATGACCTTGGCCAGAGGTGCTAAGCAGTTGGTGGTGCAGGAGGCATTGCTGATGATCTCGAGGCTGTTGTCATACT
TCTCACGGTTTACGCCCATCATGAACATGGGGGCGTCAGCAGAGGGAGCAGAGATTATGATCCTTTTGGCTCCTCCCTGC
AAG

Alignment

ORF - retro_nleu_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPLRGPSDACFTT-FLMSSYLAGFSRRQVRSTTDTLAVGTRKAMPVSFPFSSGMTLPTALAAPVEAGMMF
          MPL.GPSDACFT..FLMSSYLAGFSR.QVRSTT.TL.VGTRKA.PVSF.FSSGMTL.TALAAP.EAGMMF
Retrocopy MPLKGPSDACFTI<FLMSSYLAGFSRWQVRSTTNTLVVGTRKALPVSFLFSSGMTLSTALAAPGEAGMMF

Parental  WRAPRPSRH-SFPEGPSTVFWVAVMAWTVEPHPSTIPKLSWMTLARGAKQLVVQEALLQTKRLLSYFSWF
          WRA.RPS.H.SFPEG.STVFWVA.MAWTV...PS.IPKLSWMTLARGAKQLVVQEALL...RLLSYFS.F
Retrocopy WRALRPS-H>SFPEGLSTVFWVAAMAWTVVMSPSMIPKLSWMTLARGAKQLVVQEALLMISRLLSYFSRF

Parental  TPMTNMGASAEGAEMMTLLAPPCK
          TP..NMGASAEGAE.M.LLAPPCK
Retrocopy TPIMNMGASAEGAEIMILLAPPCK

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_405 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 1 parental gene, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000004194	41 retrocopies	retro_nleu_1019, retro_nleu_1162, retro_nleu_1316, retro_nleu_1514, retro_nleu_154, retro_nleu_1587, retro_nleu_1596, retro_nleu_1656, retro_nleu_1730, retro_nleu_1731, retro_nleu_1750, retro_nleu_186, retro_nleu_1861, retro_nleu_1863, retro_nleu_1864, retro_nleu_1865, retro_nleu_1866, retro_nleu_1867, retro_nleu_1869, retro_nleu_1945, retro_nleu_206, retro_nleu_2166, retro_nleu_2174, retro_nleu_2276, retro_nleu_2432, retro_nleu_2467, retro_nleu_2671, retro_nleu_2684, retro_nleu_2745, retro_nleu_2980, retro_nleu_306, retro_nleu_405 , retro_nleu_438, retro_nleu_459, retro_nleu_489, retro_nleu_541, retro_nleu_599, retro_nleu_626, retro_nleu_783, retro_nleu_810, retro_nleu_995,