RetrogeneDB ID: retro_nleu_1014

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:19497465..19498355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COIL
• Ensembl ID: ENSNLEG00000008026
• Aliases: None
• Description: None

Sequence

>retro_nleu_1014
TCAAAGGAAGAACCCTCTACCAAAAACACAACTGCAGACAAACTGGCTACAAAACCTGGCTTTAGCCTTACCCCCAGCAA
TGGCGGACCTCTGGAACAACGTCTTGTAGTTCAGACTCTAGTTCAGAGTCAGATGACCAATGCATGATGTCATTGAGCAC
CCCGGAGTGTGCTGCTGGTTTCTTAAAGACAGTGGGCCTTTTTGCAGGAAGAGGTTGTCCAGGCCCAGGGCTGTCATCAC
AGAGTGAAGGTGCTGCTGGATGGAGGCGTTCTGGCTCAAATGGTGATGGACAGGCTCCTGGTCCTTCTCCCAGTGTGTCT
CTCCCCGCTAGTTTAGGAAGAGGATGGGGTAGAGGAGAGAACCTTTTTTCTTGGAAGGGAGCTAGGGGATGGGGCATGCG
GAGGAGAGGTCGAGGACGAGGGCATCCTGTTTCCTGTGTTGTAAATAGAAGCATTGACAACCAGAGGCAACAGCAATTAA
ATGACGTGGTAACAAATTCATCTACTATTATCCACAATCCAGTAGAGACACACAAGAAGGACTATAGTCTGTTACCACTG
TTAGCAGCTGCCTCTCTAGTTGGAGAAAAGATTGCATTTAAGCTTTTGGAACTAACATCCAGTTACTCTCCTGATGTCTC
TGACTACAAGGAAGGAAGAATATTAAGCCACAACCCAGAGACCCAGCAAGTAGATACAGAAATTCTTTCATTCTTACCTG
CCTTGAGAGAACCTGGGAAATTTGATTTAGTTTATCACAATGAAAATGGAATCGAGGTAGTGGAGTACACTGTGACACAG
GAGAGCAAGATCACTGTATTTTGGAGAGAGTTGATTGACCCAAGACTGATAATTGAATCTCCAAGTAACACACCAAGCGC
AGAACCTGCC

Alignment

ORF - retro_nleu_1014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.93 %
• Parental protein coverage: 51.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKEEPSTKNTTADKLAIKLGFSLTPSKG-KTSGTTSSSSDSSSESDDQCVMSSSIPECAAGFLKTLGLFA
          SKEEPSTKNTTADKLA.K.GFSLTPS.G..TSGTTS.SSDSSSESDDQC.MS.S.PECAAGFLKT.GLFA
Retrocopy SKEEPSTKNTTADKLATKPGFSLTPSNG<RTSGTTSCSSDSSSESDDQCMMSLSTPECAAGFLKTVGLFA

Parental  GRGRPGPGLSSQTAGAAGWRRSGSNGGGQAPGPSPSVSLPAGLGRGWGREENLFSWKGARGRGMRGRGRG
          GRG.PGPGLSSQ..GAAGWRRSGSNG.GQAPGPSPSVSLPA.LGRGWGR.ENLFSWKGARG.GMR.RGRG
Retrocopy GRGCPGPGLSSQSEGAAGWRRSGSNGDGQAPGPSPSVSLPASLGRGWGRGENLFSWKGARGWGMRRRGRG

Parental  RGHPVSCVVNRSTDNQRQQQLNDVVTNSSTIIQNPVETPKKDYSLLPLLAAAPQVGEKIAFKLLELTSSY
          RGHPVSCVVNRS.DNQRQQQLNDVVTNSSTII.NPVET.KKDYSLLPLLAAA..VGEKIAFKLLELTSSY
Retrocopy RGHPVSCVVNRSIDNQRQQQLNDVVTNSSTIIHNPVETHKKDYSLLPLLAAASLVGEKIAFKLLELTSSY

Parental  SPDVSDYKEGKILSHNPETQQVDIEILSSLPALREPGKFDLVYHNENGAEVVEYAVTQESKITVFWRELI
          SPDVSDYKEG.ILSHNPETQQVD.EILS.LPALREPGKFDLVYHNENG.EVVEY.VTQESKITVFWRELI
Retrocopy SPDVSDYKEGRILSHNPETQQVDTEILSFLPALREPGKFDLVYHNENGIEVVEYTVTQESKITVFWRELI

Parental  DPRLIIESPSNTSSKEPA
          DPRLIIESPSNT.S.EPA
Retrocopy DPRLIIESPSNTPSAEPA

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_1014 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008740	1 retrocopy	retro_chof_1121,
Callithrix jacchus	ENSCJAG00000013960	1 retrocopy	retro_cjac_2240,
Dasypus novemcinctus	ENSDNOG00000023961	1 retrocopy	retro_dnov_1986,
Echinops telfairi	ENSETEG00000003687	1 retrocopy	retro_etel_1537,
Nomascus leucogenys	ENSNLEG00000008026	1 retrocopy	retro_nleu_1014 ,
Oryctolagus cuniculus	ENSOCUG00000011345	1 retrocopy	retro_ocun_1798,
Pongo abelii	ENSPPYG00000008248	1 retrocopy	retro_pabe_305,
Tupaia belangeri	ENSTBEG00000008882	4 retrocopies	retro_tbel_2118, retro_tbel_3549, retro_tbel_3961, retro_tbel_838,