RetrogeneDB ID: retro_nleu_912

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:25255982..25256899(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL2
• Ensembl ID: ENSNLEG00000004370
• Aliases: None
• Description: None

Sequence

>retro_nleu_912
ATGGCCCTGTGGGCACTGACCTGCGCTCTGCACTCTCTGAGCCTGGCACCCCCGACCGTTGCCACTCCTGTCCCGAGTCT
GTTCCCTGCCTCCCAGGTGATGAACAATGCCCTCTTCCAATGGCCCTCTGCCTTGATGTTGCTCCCCTGCCACCAAATCC
TTACTTCTATGGCCCTTAGTGCCAACTTTGTGTCTTGAAAGAGTCATACCAAGTACACCATTAAACCAGTGAAGATGAGG
AAGTCTGGGGGTGAAGACCACACAGGCCAGATCTGGGTGCATGGTATTGGCAGAGGCCACAAGCAACATTATTGCATGAT
TGACTTTTGTGTTTCTGGCCTCAGGAGGAGACCAAGTCAGGACCCTTTGAGGAGAAGGTTATCCAAATTCACTGTGATCC
CTGTAGGTCAGCAGACATAGGTCTGGTTGCTGGGGGCAGCCAGAAACACTGGATCATCGCCACAGAAAACATACAGGCTG
GAGATACAATCCTGAACTCTAACCACATAGGCCAAATGGCAGTTGCTGCTTAGGAAGGGGATGCATATCCACTGGGGGCT
CTGCCTGTGGGGACCCTCATCAACAACATGGAAAGTGAGCCAGGCCGGGGTGCCCAGTATATCTGAGCTGCAGAGAAGTG
TGGTGTGCTACTGTGGAAGGTGAATGGCACAGCCATTATCCAGCTGCCCTCTAAGAGGCAGATGCAGGTGCTGGAAACAT
GCATAGCAACAATAGGCTGAGTATCCAACACTGATCATAACAAACAGGTCACTGGCAGAGCAGGTCACAACCGTTGGCTG
GGCAAGAGGCCTTCCAGTGGGCTATGGCACTGCAAGGGGTGTTGGGCTGGCCGAAAGATTTGGCCACTACCCTTCATGAA
GAGTTATGTGAAGCTGCCTTCTGATGCTGCCCAAAGC

Alignment

ORF - retro_nleu_912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALWALTRLLRSLSLAPPTVAAPAPSVFPAAQMMNNGLLQQPSALMLLPCRPVLTSVALNANFVSWKSRT
          MALWALT..L.SLSLAPPTVA.P.PS.FPA.Q.MNN.L.Q.PSALMLLPC...LTS.AL.ANFVS.KS.T
Retrocopy MALWALTCALHSLSLAPPTVATPVPSLFPASQVMNNALFQWPSALMLLPCHQILTSMALSANFVS*KSHT

Parental  KYTIAPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDF-LRFRP-EETKSGPFEEKVIQVRYDPCRSAD
          KYTI.PVKMRKSGG.DHTG.I.VHGIG.GHKQ.Y.MIDF.L.F.P.EETKSGPFEEKVIQ...DPCRSAD
Retrocopy KYTIKPVKMRKSGGEDHTGQIWVHGIGRGHKQHYCMIDF<LCFWPQEETKSGPFEEKVIQIHCDPCRSAD

Parental  IALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGDAHPLGALPVGTLINNVESEPGRGAQYIR
          I.LVAGGS.K.WIIATEN.QAGDTILNSNHIG.MAVAA.EGDA.PLGALPVGTLINN.ESEPGRGAQYI.
Retrocopy IGLVAGGSQKHWIIATENIQAGDTILNSNHIGQMAVAA*EGDAYPLGALPVGTLINNMESEPGRGAQYI*

Parental  AAGTCGVLLRKVNGTAIIQLPSKRQMQVLETCVATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHRK
          AA..CGVLL.KVNGTAIIQLPSKRQMQVLETC.AT.G.VSN.DHNK.V.G.AG.NRWLGKRP.SG.WH.K
Retrocopy AAEKCGVLLWKVNGTAIIQLPSKRQMQVLETCIATIG*VSNTDHNKQVTGRAGHNRWLGKRPSSGLWHCK

Parental  GGWAGRKIRPLPPMKSYVKLPSAAAQS
          G.WAGRKI.PLP.MKSYVKLPS.AAQS
Retrocopy GCWAGRKIWPLPFMKSYVKLPSDAAQS

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_912 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005134	1 retrocopy	retro_acar_136,
Callithrix jacchus	ENSCJAG00000005116	1 retrocopy	retro_cjac_3318,
Homo sapiens	ENSG00000112651	1 retrocopy	retro_hsap_1039,
Gorilla gorilla	ENSGGOG00000010552	1 retrocopy	retro_ggor_820,
Macaca mulatta	ENSMMUG00000002450	1 retrocopy	retro_mmul_827,
Nomascus leucogenys	ENSNLEG00000004370	1 retrocopy	retro_nleu_912 ,
Otolemur garnettii	ENSOGAG00000034421	2 retrocopies	retro_ogar_1582, retro_ogar_1842,
Pongo abelii	ENSPPYG00000016630	1 retrocopy	retro_pabe_871,
Pan troglodytes	ENSPTRG00000018186	1 retrocopy	retro_ptro_709,
Rattus norvegicus	ENSRNOG00000018057	1 retrocopy	retro_rnor_555,