RetrogeneDB ID: retro_nleu_2399

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397352.1:4119759..4120516(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNASEH1
• Ensembl ID: ENSNLEG00000015400
• Aliases: None
• Description: None

Sequence

>retro_nleu_2399
CTGTCCCTGGCCCACAGAGTCACCTTGATAGCTGTGTGCTGCCACAGGGACTGCTGCAGCCTCAGGATGGTCTATGCTGT
GGGGAGGGCCTGCAGGACTGGGGTCTTTCTGACCTGGAATGAATGTAGAGCATAGGTGGACCTATTTCCTGCTGCCAGAT
TTAAGAAGTTTGTCACAGAAAATGAGGCCTGGGCCTTTGTCAGGAAATCTGCAAGCCCAGAAGGTTCAGAAGGGCAGAAA
AATAAACATGTACGAGAATCACAAACGAAAGCCGGCAAGGGACTGCGTGAGCCACTGAATGGAGATGGAGATGAAAGTGC
GGAGTCTTGTGCAAAGCCTGTGAAGCAAATCACAGAGCCGGCGCCTCGAGTGAGCAGAGACATTTTCTTACATCGGAGGC
TTTATTGTCGTCTACACTGATGGCTGCTGCTCCAGTAACAGGTGGAGGAGAGCACTAGTGGGAACTGACGTTTACTGGGG
GCCATGCCATCCTTTAAATGTAGGCATTAGACTTCCTGGGTGACAGACAAACCAAAGAGCAGAAAATCATGCAGCCTGCA
GCACCATTGAACAAGCAAAGGCTGAAAACATCAATAAATTGGTTCTGTACACAGATAGTATGTTTGCTATAAATGGTATA
ACTAACTGGGTTCAAGGTAGGAAGAGGAACAGGTGGAAGACAAGTACAGGGAAAGAGGTGACAAACAAAGAGGACTTTGC
GGCACTGGAGAAGCTCAGTCGAGGCATGGACATTCAG

Alignment

ORF - retro_nleu_2399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.89 %
• Parental protein coverage: 88.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFLAHRVALAAVPCRRGTRGFGMFYAVRRGRKTGVFLTWTECKAQVDRFPAARFKKFATEDEAWAFVRKS
          L.LAHRV.L.AV.C.R......M.YAV.R...TGVFLTW.EC.A.VD.FPAARFKKF.TE.EAWAFVRKS
Retrocopy LSLAHRVTLIAVCCHRDCCSLRMVYAVGRACRTGVFLTWNECRA*VDLFPAARFKKFVTENEAWAFVRKS

Parental  ASPEVSEGQENQHGQESETKASKRLREPLDGDGDGDESAEPYAKHMKPSVEPAPPVSRDTFSYM-GDFVV
          ASPE.SEGQ.N.H..ES.TKA.K.LREPL...GDGDESAE..AK..K...EPAP.VSRD.F....G..VV
Retrocopy ASPEGSEGQKNKHVRESQTKAGKGLREPL--NGDGDESAESCAKPVKQITEPAPRVSRDIFLHR>GFIVV

Parental  VYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTDS
          .YTDGCCSSN..RR...G..VYWGP.HPLNVGIRLPG.QTNQRAE.HAAC..IEQAK..NINKLVLYTDS
Retrocopy -YTDGCCSSNRWRRALVGTDVYWGPCHPLNVGIRLPG*QTNQRAENHAACSTIEQAKAENINKLVLYTDS

Parental  MFTINGKLSHLISSGRTQMGTGKVTLVSKSEDFGVSLLLLRSYAMQ
          MF.ING.........R....T.....V...EDF.....L.R....Q
Retrocopy MFAINGITNWVQGRKRNRWKTSTGKEVTNKEDFAALEKLSRGMDIQ

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_2399 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008547	6 retrocopies	retro_chof_158, retro_chof_1653, retro_chof_1836, retro_chof_2224, retro_chof_485, retro_chof_843,
Callithrix jacchus	ENSCJAG00000035450	1 retrocopy	retro_cjac_3811,
Echinops telfairi	ENSETEG00000012674	1 retrocopy	retro_etel_1286,
Homo sapiens	ENSG00000171865	2 retrocopies	retro_hsap_1814, retro_hsap_300,
Gorilla gorilla	ENSGGOG00000034822	2 retrocopies	retro_ggor_2175, retro_ggor_336,
Macropus eugenii	ENSMEUG00000003610	1 retrocopy	retro_meug_1172,
Macaca mulatta	ENSMMUG00000014475	2 retrocopies	retro_mmul_544, retro_mmul_799,
Monodelphis domestica	ENSMODG00000014491	1 retrocopy	retro_mdom_593,
Nomascus leucogenys	ENSNLEG00000015400	2 retrocopies	retro_nleu_2399 , retro_nleu_2959,
Pongo abelii	ENSPPYG00000025873	1 retrocopy	retro_pabe_18,
Pan troglodytes	ENSPTRG00000011614	1 retrocopy	retro_ptro_244,
Pteropus vampyrus	ENSPVAG00000002070	1 retrocopy	retro_pvam_144,
Sarcophilus harrisii	ENSSHAG00000013051	1 retrocopy	retro_shar_245,