RetrogeneDB ID: retro_nleu_899

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:2992099..2992626(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL40
• Ensembl ID: ENSNLEG00000005372
• Aliases: None
• Description: None

Sequence

>retro_nleu_899
ACCCACCAGCGAGCTTCAGTGTTGTCCTCCTAGGAACTCATTCCTGTGAGAGCAGAACCTCTTTGAGAGCAGAAGATGAA
TCCTAAAAAAGACCAAGCAGGAAAGGGCTGCTTGAAACATAAAATATGAAAACTGGAAAAGGCTAGCCAAGAGCTCATTC
TTGTTGCAGATTTTATTAGCTTTGTGAAGTTCTTGGATAAAGCAAGCTAGTGGCCTCAGGTGGAGCTCTCCTTGGAGGAG
AGTGAGTAGAGAGCTCTGCTTCTGATGAGTGGTCCCTGTACAAGCAGCGAGACTACACTATGGACAGGGACACCATCAAG
GCCGTGCTGGAGGCCCAGCAGGAAGCTCTGCAGGAGCTACCACTCGAGTCCCCTGAGTTCCCCACTGAGGCCATCAAGTG
GGACTGCAGCATGTTCCCCTTTGAGTGGGAAGGTCCAGATTACACACTATGGGTCTCTAACTACCAGCCCCCCAAAGGCA
GGTACAATGACATCACCAAGATGTACACATACGTAGAGCTCAAGAGA

Alignment

ORF - retro_nleu_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.48 %
• Parental protein coverage: 85.92 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  THQRASLLSFWELIPMRSEPPRKKKKVDPKKDQEAKERLKRKIRKLEKATQELIPIEDFITPLQFLDKAR
          THQRAS.LS..ELIP.R.EP.....K..PKKDQ..K..LK.KI.KLEKA.QELI...DFI....FLDKA.
Retrocopy THQRASVLSS*ELIPVRAEP-L*EQKMNPKKDQAGKGCLKHKI*KLEKASQELILVADFISFVKFLDKAS

Parental  ERPQVELTFEETERRAVLLK-KWSLYKQQEHKTERDTIRAMLEAQQEALEELRLESPKLHAEAIKRDPNL
          ..PQVEL..EE.E.RA.LL...WSLYKQ......RDTI.A.LEAQQEAL.EL.LESP....EAIK.D...
Retrocopy *WPQVELSLEESE*RALLLM<EWSLYKQRDYTMDRDTIKAVLEAQQEALQELPLESPEFPTEAIKWDCSM

Parental  FPFEKEGPHYTPPIPNYQPPEGRYNDITKVYTQVEFKR
          FPFE.EGP.YT....NYQPP.GRYNDITK.YT.VE.KR
Retrocopy FPFEWEGPDYTLWVSNYQPPKGRYNDITKMYTYVELKR

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_899 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001053	1 retrocopy	retro_acar_149,
Ailuropoda melanoleuca	ENSAMEG00000011421	1 retrocopy	retro_amel_257,
Callithrix jacchus	ENSCJAG00000001584	1 retrocopy	retro_cjac_3220,
Equus caballus	ENSECAG00000009876	1 retrocopy	retro_ecab_687,
Homo sapiens	ENSG00000185608	1 retrocopy	retro_hsap_1020,
Gorilla gorilla	ENSGGOG00000012336	1 retrocopy	retro_ggor_807,
Myotis lucifugus	ENSMLUG00000002456	1 retrocopy	retro_mluc_1950,
Macaca mulatta	ENSMMUG00000016081	1 retrocopy	retro_mmul_57,
Mustela putorius furo	ENSMPUG00000003865	1 retrocopy	retro_mputfur_394,
Nomascus leucogenys	ENSNLEG00000005372	1 retrocopy	retro_nleu_899 ,
Pongo abelii	ENSPPYG00000011578	1 retrocopy	retro_pabe_857,
Rattus norvegicus	ENSRNOG00000049686	1 retrocopy	retro_rnor_1624,
Tarsius syrichta	ENSTSYG00000014747	1 retrocopy	retro_tsyr_1589,