RetrogeneDB ID: retro_nleu_488

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397266.1:26627208..26627732(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSNLEG00000015577
• Aliases: None
• Description: None

Sequence

>retro_nleu_488
ATGCATGTCTCTGCAGACAAAGATGAACACAGTATTGAAATGCATTTGCCTTATACAGCTAAAGCCATGGAAATCCATAA
GGATGAGTTTACCATTATTCCTGTACTGGTTGGAGCTCTGAGTGAGTCAAAAGAACAGGAATTCAGAAAACTCTTCAGTA
AATATCTAGCAGATCCTAGTAATTTCTTTGTGGTTTCTTCTGATTTTTGCCATTGGGGTCAAACATTCCGTTACAGTTAC
TATGATGAATCCCAGGGGGAGACTTATAGATCCGTTGAATATCTAGATAAAATGGGTATGAGTATTATAGAACAATTAGA
CCCTGTATCTTTTAGCAATTACTTGAGGAAACACCATAATACTATATGTGGAAGACATCCCTTTAGGGTGTTAAATGCTA
TCACGGAGCTCCAGAAGAATGGAAGAATATGAGCTTTTCCTTTTTGAATTATGCCCAGCCAAGCCAGTGTAGAAACTGGC
AAGACAGTTCAGTGAGTTACGCAGCTGGAGCACTCACGGTCCAC

Alignment

ORF - retro_nleu_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 63.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLQTDEDEHSIEMHLPYTAKAMESHKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSSDFC
          M....D.DEHSIEMHLPYTAKAME.HKDEFTIIPVLVGALSESKEQEF.KLFSKYLADPSN.FVVSSDFC
Retrocopy MHVSADKDEHSIEMHLPYTAKAMEIHKDEFTIIPVLVGALSESKEQEFRKLFSKYLADPSNFFVVSSDFC

Parental  HWGQRFRYSYYDESQGEIYRSIEHLDKMGMSIIEQLDPVSFSNYLKKYHNTICGRHPIGVLLNAITELQK
          HWGQ.FRYSYYDESQGE.YRS.E.LDKMGMSIIEQLDPVSFSNYL.K.HNTICGRHP..V.LNAITELQK
Retrocopy HWGQTFRYSYYDESQGETYRSVEYLDKMGMSIIEQLDPVSFSNYLRKHHNTICGRHPFRV-LNAITELQK

Parental  NG-MNMSFSFLNYAQSSQCRNWQDSSVSYAAGALTVH
          NG..NMSFSFLNYAQ.SQCRNWQDSSVSYAAGALTVH
Retrocopy NG<KNMSFSFLNYAQPSQCRNWQDSSVSYAAGALTVH

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_488 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007771	1 retrocopy	retro_amel_1500,
Equus caballus	ENSECAG00000019946	1 retrocopy	retro_ecab_401,
Echinops telfairi	ENSETEG00000007994	1 retrocopy	retro_etel_561,
Felis catus	ENSFCAG00000001385	1 retrocopy	retro_fcat_642,
Homo sapiens	ENSG00000162959	2 retrocopies	retro_hsap_2507, retro_hsap_3522,
Myotis lucifugus	ENSMLUG00000016108	1 retrocopy	retro_mluc_1923,
Mus musculus	ENSMUSG00000058704	1 retrocopy	retro_mmus_834,
Nomascus leucogenys	ENSNLEG00000015577	1 retrocopy	retro_nleu_488 ,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Otolemur garnettii	ENSOGAG00000010975	3 retrocopies	retro_ogar_1860, retro_ogar_2049, retro_ogar_3050,
Pongo abelii	ENSPPYG00000012511	1 retrocopy	retro_pabe_2910,