RetrogeneDB ID: retro_nleu_2194

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397333.1:10794498..10795973(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTNNBL1
• Ensembl ID: ENSNLEG00000006291
• Aliases: None
• Description: None

Sequence

>retro_nleu_2194
GAAGAGGAAATGATTGTGGTGGAAGAAGCAGAGGATGACAAAAAATGGCTGCTTCAGATTATTGACACAGAGGGTGAGGA
GGAAGAGAAAGAGGAGGAGCCATTGGATGAAAGCTCAGTGAAGAAAACGATCCTCACATTTGAATAGTGAGCATATAAAA
ACCAAGAATTGCGGATTAAGTTTCCAGACAATCCAGAGAAGTTCATGGAATCCCAACTGGACCTACATGACATCATTCGG
AAGATGCACGTGGTGGCCACCATGCCAGACCTGTACCTTTTGCTGGAGCTGAATGCTGTGCAGTCACCTCTTGGGTTGCT
TGGACACAATAATACAGATGTGTCCATAGCTGGGGTTGATTTGAGTCAGGAATTAACAGATATAGACATCTTCTATGAGA
GTGAAGAGGAAGCAGAAGTACTCATTGATGCTCTGGTGGATGGGCAGGTGATAGTGCTGCTGGTGCAGAATGTGGAGCGC
CTGGATGAGTCTGTGAAGGAGCAGGCCAATGGTGTCCATAACACTCTTGTTATTGTGGAAAACATGGCTGAGTTCTAGCC
GGAGATGTGTACAAAAGGTGCCCAGCAGGGTCTTCCTCAGTGGCTGTTGAAGAGGCTGAAGGCAAAGAAGCCTTTTGATG
CCAACAAACTGTATTGCAGTGAAATGCAGGCCATATTGCTCCAGGACAACGATGAAAACAGGAAATTGCTTGGGGAGCTG
GATGGAATTGATGCACTTCTTCAGCAGTTATCTGTGTTTAAAAGACACAATCCCAGCACAGCAAAGGAGCAGGAGATGAT
GGAGAATCTGTTTGATTCACTCTGCTTCTAACTAATGCTCATTTCAAATCGTGAGCACTTCCTGAAAGGCGAGGGTCTTC
AGGTGATGAATCTCATGCTCAGGGAAGAAGAAGATCTCACGGAGTGGGGTCCTGAAAGTGCTGATTGCACCCGAGGGCAT
CCACAACTGCGGTAAATTTGTTGACATTCTTGGCTTATGAATCATCTTTCCCCTCTTTATGGAATTTCCCAGGAAGATCA
AGAAAGTGGGTACCACTGACAAGGAACACAAAGAGCGTGTCTGTTCCATTCTGGCTTCCCTTTTGGGGAACCTGAGAGGG
CATCAGTGAACCCAGCTTCTGAATAAATTCACTGAAAATGACAGTGAATAGGCTGACAGACTAATGGAGTTGCATTTTCA
ATATCTGGATGCAATGCAGGTGGCAGACAAGAGGAATGAAGAGGAAAAACATGACATGGTCCAGCGTGGAGAGACCATAG
ACAGTGACACGGGGGGATGAGTTCTACCTCCAGTGCTTGGATGCAGGGCTCTTTGTTCTCCAGTGCATCTGCTGCATTAT
GGCCAAGATCTGCAATGCCAATGTCCCCCAGATTTGCCAGAGGGTTCACCAGATCCTAAACATGTGAGGACGCTCCATCA
AAATTTTCAGGCATATCATCAAGGGGTATGCGGAG

Alignment

ORF - retro_nleu_2194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.12 %
• Parental protein coverage: 88.1 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEEMTVVEEADDDKKRLLQIIDRDGEEEEEEEEPLDESSVKKMILTFEKRSYKNQELRIKFPDNPEKFME
          EEEM.VVEEA.DDKK.LLQIID..GEEEE.EEEPLDESSVKK.ILTFE...YKNQELRIKFPDNPEKFME
Retrocopy EEEMIVVEEAEDDKKWLLQIIDTEGEEEEKEEEPLDESSVKKTILTFE**AYKNQELRIKFPDNPEKFME

Parental  SELDLNDIIQEMHVVATMPDLYHLLVELNAVQSLLGLLGHDNTDVSIAVVDLLQELTDIDTLHESEEGAE
          S.LDL.DII..MHVVATMPDLY.LL.ELNAVQS.LGLLGH.NTDVSIA.VDL.QELTDID...ESEE.AE
Retrocopy SQLDLHDIIRKMHVVATMPDLY-LLLELNAVQSPLGLLGHNNTDVSIAGVDLSQELTDIDIFYESEEEAE

Parental  VLIDALVDGQVVALLVQNLERLDESVKEEADGVHNTLAIVENMAEFXKQPCQEGAAIPNLQIKKSQREAK
          VLIDALVDGQV..LLVQN.ERLDESVKE.A.GVHNTL.IVENMAEF....C..GA.....Q.......AK
Retrocopy VLIDALVDGQVIVLLVQNVERLDESVKEQANGVHNTLVIVENMAEF*PEMCTKGAQQGLPQWLLKRLKAK

Parental  MPFDANKLYCSEVLAILLQDNDENRELLGELDGIDVLLQQLSVFKRHNPSTAEEQEMMENLFDSLCSCLM
          .PFDANKLYCSE..AILLQDNDENR.LLGELDGID.LLQQLSVFKRHNPSTA.EQEMMENLFDSLC..LM
Retrocopy KPFDANKLYCSEMQAILLQDNDENRKLLGELDGIDALLQQLSVFKRHNPSTAKEQEMMENLFDSLCF*LM

Parental  LSSNRERFLKGEGLQLMNLMLRE-KKISRSSALKVLDHAMIGPEGTDNCHKFVDILGLRTIFPLFMKSPR
          L.SNRE.FLKGEGLQ.MNLMLRE.KKISRS..LKVL....I.PEG..NC.KFVDILGL..IFPLFM..PR
Retrocopy LISNREHFLKGEGLQVMNLMLRE>KKISRSGVLKVL----IAPEGIHNCGKFVDILGL*IIFPLFMEFPR

Parental  KIKKVGTTEKEHEEHVCSILASLLRNLRGQQRTRLLNKFTENDSEKVDRLMELHFKYLGAMQVADKKIEG
          KIKKVGTT.KEH.E.VCSILASLL.NLRG.Q.T.LLNKFTENDSE..DRLMELHF.YL.AMQVADK..E.
Retrocopy KIKKVGTTDKEHKERVCSILASLLGNLRGHQ*TQLLNKFTENDSE*ADRLMELHFQYLDAMQVADKRNEE

Parental  EKHDMVRRGEIIDNDT-EEEFYLRRLDAGLFVLQHICYIMAEICNANVPQIRQRVHQILNMRGSSIKIVR
          EKHDMV.RGE.ID.DT...EFYL..LDAGLFVLQ.IC.IMA.ICNANVPQI.QRVHQILNM.G.SIKI.R
Retrocopy EKHDMVQRGETIDSDT>GDEFYLQCLDAGLFVLQCICCIMAKICNANVPQICQRVHQILNM*GRSIKIFR

Parental  HIIKEYAE
          HIIK.YAE
Retrocopy HIIKGYAE

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_2194 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132792	1 retrocopy	retro_hsap_4819,
Gorilla gorilla	ENSGGOG00000000614	1 retrocopy	retro_ggor_3003,
Macropus eugenii	ENSMEUG00000013001	1 retrocopy	retro_meug_910,
Myotis lucifugus	ENSMLUG00000015803	1 retrocopy	retro_mluc_177,
Macaca mulatta	ENSMMUG00000017224	1 retrocopy	retro_mmul_2571,
Nomascus leucogenys	ENSNLEG00000006291	1 retrocopy	retro_nleu_2194 ,
Pongo abelii	ENSPPYG00000010989	1 retrocopy	retro_pabe_3747,
Pan troglodytes	ENSPTRG00000023688	1 retrocopy	retro_ptro_3208,