RetrogeneDB ID: retro_nleu_1819

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397312.1:654552..655539(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM1
• Ensembl ID: ENSNLEG00000013055
• Aliases: None
• Description: None

Sequence

>retro_nleu_1819
ATGACCACCCAGCAGCTCGTCCTCCAGGGCCCGGGCCCGTGGGGCTTCCGTTTCGTGGGTGTCAAGGACTTTGAGCAGCC
TCTCACCATTTCCCGGGTCACTCCTGGAAGCAAGGTGGCTCTAGCTAATTTATGTATCAGAGACGTAATCACAGCCATTG
ATGGGGAAAATTCTAGCAATATGACACATTTGGAAGCTCAGAACAGAATCAAAGGCTGCAAAGACAACATGACTCTCACT
GTAGCCAGATCCGAACATAAAGTCTGGTCTCCTCTGGTGACGGAGGAAGAGAAGTGTCGTCCATACAAGATGAATTTAGC
CTCTGAACCCCAGGAGGCCCTGCACATAGGAAGCGCCCACAACCAAAGTTCCATGCCCTTTACCACCTCGCCTGCCTCCA
GCACTAACGCCAGGGTCATCACAAACCAGTACAACCACCCAGCTGGCCTCTACTCTTCTGAAAATATCTCCAACTTCAAC
AACGCCCTGGAGTCAAAGACTGCTGCCAGTGGGGTGGAGGCGAACGGCAGACGGTTAGACCATGCTCAGCCTCCAACCAG
CCTTGTCATCGACAAAGAATCTGAAGTTTGCAAGATGCTTCAGGAGAAACGGGAGTTGAATGAGCCCCCAAAACAGTCCG
TGTCTTTTCTGGTTTTGCAGGAAATCCTGGAGTCTGAAGAAAAAAAGGATCCCAACAAGCCCTGAGGATTCAGAAGTGTT
AAAGCTCCCGTCACTAAAGTGGCTGCATTGATTGGAAATGCTCAGAAGTTTCCCACGTGTGACATATGTGGCCCTGGAAT
TGTCAGTGTGTTCGTGAAGCTGCAGGACCATCACCGCCACCCCGAGTGTTACGTGCACACTGACTGTGGCACCAACCTGA
AACAGAGGGGCCATTTCTTTGTGGAGGATCAAATCTACTGTGAGAAGCATGCCTGGGAATGAGTCGCACCACTCGAGGGC
TACGAAGTGGTCACCGTGTTCCCCAAG

Alignment

ORF - retro_nleu_1819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTQQIVLQGPGPWGFRLVGGKDFEQPLAISRVTPGSKAALANLCIGDVITAIDGENTSSMTHLEAQNRI
          MTTQQ.VLQGPGPWGFR.VG.KDFEQPL.ISRVTPGSK.ALANLCI.DVITAIDGEN.S.MTHLEAQNRI
Retrocopy MTTQQLVLQGPGPWGFRFVGVKDFEQPLTISRVTPGSKVALANLCIRDVITAIDGENSSNMTHLEAQNRI

Parental  KGCTDNLTLTVARSEHKVWSPLVTEEGKRHPYKMNLASEPQEVLHIGSAHNRSAMPFTASPASSTTARVI
          KGC.DN.TLTVARSEHKVWSPLVTEE.K..PYKMNLASEPQE.LHIGSAHN.S.MPFT.SPASST.ARVI
Retrocopy KGCKDNMTLTVARSEHKVWSPLVTEEEKCRPYKMNLASEPQEALHIGSAHNQSSMPFTTSPASSTNARVI

Parental  TNQYNNPAGLYSSENISNFNNALESKTAASGVEANSRPLDHAQPPSSLVIDKESEVYKMLQEKQELNEPP
          TNQYN.PAGLYSSENISNFNNALESKTAASGVEAN.R.LDHAQPP.SLVIDKESEV.KMLQEK.ELNEPP
Retrocopy TNQYNHPAGLYSSENISNFNNALESKTAASGVEANGRRLDHAQPPTSLVIDKESEVCKMLQEKRELNEPP

Parental  KQSTSFLVLQEILESEEKGDPNKPSGFRSVKAPVTKVAASIGNAQKLPMCDKCGIGIVGVFVKLRDRHRH
          KQS.SFLVLQEILESEEK.DPNKP.GFRSVKAPVTKVAA.IGNAQK.P.CD.CG.GIV.VFVKL.D.HRH
Retrocopy KQSVSFLVLQEILESEEKKDPNKP*GFRSVKAPVTKVAALIGNAQKFPTCDICGPGIVSVFVKLQDHHRH

Parental  PECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVTPPEGYEVVTVFPK
          PECYV.TDCGTNLKQ.GHFFVEDQIYCEKHA.E.V.P.EGYEVVTVFPK
Retrocopy PECYVHTDCGTNLKQRGHFFVEDQIYCEKHAWE*VAPLEGYEVVTVFPK

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_1819 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819 , retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,