RetrogeneDB ID: retro_nleu_3062

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397693.1:97342..98074(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PMM2
• Ensembl ID: ENSNLEG00000010062
• Aliases: None
• Description: None

Sequence

>retro_nleu_3062
ATGGCAGCACCCGGCCCAGTGCTCTGCCTTTTGGACGTTGATGGGACCCTGACCACCCCGCAGCAGAAAATTACCAAAGA
AATGGATGACTTCCTACAAAAATTGAGGCAGAAGATCAAAATCGGAGTGGTAGGCAGGTTGGACTTTGAGGAAGTGCAGG
AGCAACTGGGAAGTGATGTGCTTGAAAAATATGATTATGCATTTCCAAAAAATGGCTTGGTAGCATACAAAGATGGGAAA
TGCTCGTGTAAATGGAATATTCAAAGTCACCTGGGTGAGGTCCTAATCCAAGATTTCATCAACTACTGCCTGAGCTACAA
TGCAAAAATTAAACTCCTGAAGAAGAGGGGTACTTTCACTGAATTCTGAAATGGGATATTAAACATGTCCCCTATTTGGA
AGAAGCTGCAGCCAAGAAGAATGCATTGAGTTCTACGAATTCAATAACAAAGAAAATGTAAGAGAAAAACTTGTAGCAGA
TCAAGGAAAGAGTTTGCAGGAGAAGGCCTCATGTTTTTCATGGGAAGCCAGGTCAGCTTTGATGTCTTTCCTGATGGATG
GGGCAAGAGGTATTGCCTGTGACATGTGAAAAACGACAGTTATAAGGCCATTTATTTCTATGGAGACAAAATCATACCAG
GTGGCAACGACCATGAGACCTTCACAGACTCCAGGACCGTGGGCTACTCCATGACGGTGCCTGAGGACACACGCAGGATC
TGTGAAGAGCTT

Alignment

ORF - retro_nleu_3062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.86 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPGPALCLFDVDGTLTAPRQKITKEMDDFLQKLRQKIKIGVVGGSDFEKVQEQLGNDVVEKYDYVFPE
          MAAPGP.LCL.DVDGTLT.P.QKITKEMDDFLQKLRQKIKIGVVG..DFE.VQEQLG.DV.EKYDY.FP.
Retrocopy MAAPGPVLCLLDVDGTLTTPQQKITKEMDDFLQKLRQKIKIGVVGRLDFEEVQEQLGSDVLEKYDYAFPK

Parental  NGLVAYKDGKLLCKQNIQSHLGEALIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPI-GRSCSQE
          NGLVAYKDGK..CK.NIQSHLGE.LIQD.INYCLSY.AKIKL.KKRGTF.EF.NG.LN.SPI.GRSCSQE
Retrocopy NGLVAYKDGKCSCKWNIQSHLGEVLIQDFINYCLSYNAKIKLLKKRGTFTEF*NGILNMSPI>GRSCSQE

Parental  ERIEFYELDKKENIRQKFVAD-LRKEFAGKGLTFSIGGQISFDVFPDGWDKRYCLRHVENDGYKTIYFFG
          E.IEFYE...KEN.R.K.VAD..RKEFAG.GL.F..G.Q.SFDVFPDGW.KRYCL.HV.ND.YK.IYF.G
Retrocopy ECIEFYEFNNKENVREKLVAD<SRKEFAGEGLMFFMGSQVSFDVFPDGWGKRYCL*HVKNDSYKAIYFYG

Parental  DKTMPGGNDHEIFTDPRTMGYSVTAPEDTRRICEVL
          DK..PGGNDHE.FTD.RT.GYS.T.PEDTRRICE.L
Retrocopy DKIIPGGNDHETFTDSRTVGYSMTVPEDTRRICEEL

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_3062 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000235	1 retrocopy	retro_cpor_810,
Homo sapiens	ENSG00000140650	2 retrocopies	retro_hsap_1869, retro_hsap_1913,
Gorilla gorilla	ENSGGOG00000010124	1 retrocopy	retro_ggor_1399,
Monodelphis domestica	ENSMODG00000005737	1 retrocopy	retro_mdom_285,
Nomascus leucogenys	ENSNLEG00000010062	1 retrocopy	retro_nleu_3062 ,
Otolemur garnettii	ENSOGAG00000016560	1 retrocopy	retro_ogar_1095,
Pongo abelii	ENSPPYG00000007084	2 retrocopies	retro_pabe_1583, retro_pabe_1584,
Pan troglodytes	ENSPTRG00000007748	2 retrocopies	retro_ptro_1249, retro_ptro_1279,
Sus scrofa	ENSSSCG00000021236	1 retrocopy	retro_sscr_329,