RetrogeneDB ID: retro_mmul_2571

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:44255157..44256249(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTNNBL1
• Ensembl ID: ENSMMUG00000017224
• Aliases: None
• Description: beta-catenin-like protein 1 [Source:RefSeq peptide;Acc:NP_001248594]

Sequence

>retro_mmul_2571
ATAGACATCTTCTATGAGAGTGAAGAGGGAGCAGAAGTACTCATTGATGCTCTGGTGGATGGGTAGGTGACAGCACTGCT
GGTGCAGAACGTGGAGCGCCTGGATGAGTCTGTGAAGGAGGAGGCCAATAGTGTCCATAACACTCTTGTTATTGTGGGAA
ACATGGCTGAGTTCTAGCTGGAGATGTGTACGAGAGGTGCCCAGCAGGGTCTTCCTCAGTGGCTGTTGAAGAGGCTGAAG
GCAAAGAAGCCTTTTGATGCCAACAAACTGTATTGCAGTGAAATGCAGGCCATATTGCTCCAGGACAACGATGAAAACAG
GAAATTGCTTGGGGAGCTGGATGGAATTGATGCACTTCTTCAGCAGTTATCTGTGTTTAAAAGACACAATCCCAGCACAG
CAAAGGAGCAGGAGATGATGGAGAATCCGTTTGATTCACTCTGCTTCTAACTAATGCTCAGTTCCAATCGTGAGCACTTC
CTGAAGGGCGAGGGTCTTCAGTTGATGAATCTCATGCTCAGGGAAAAGAAGATCTCACGGAGCAGGGTCCTGAAAGTGCT
GATTGCATCCAAGGGCGTCTACAACTGCGGTAAATTTGTTGACATTCTTGGCTTATGAACCATCTTTCCCCTCTTTATGG
AATTTCCCAGAAAGATCAAGAAAGTGGGTACCACTGACAGGGAACACAAAGAGCATGTCTGTTCCATTCTGGCTTTCCTT
TTGTGGAACCTGAGAGGGCATCAGCGAACCTGGCTTCTGAATAAATTCACTGAAAATGACAGCGAGTAGGCTGACAGACT
AATGGAGTTGCATTTTCAATATCTGGGTGCAATGCAGGTGGCAGACAAGAGGAAGGAAGGGGAAAAACATGACATGGTCC
AGTGTGGAGAGATCATAGACAGTGACATGGGGGATGAGTTCTACCTCCAGTGCTTGGATGCAGGGCTCTTTGTTCTCCAG
TGCATCTGCTGCATTATGGCCAAGATCTGCAATGCCAATGTTCCCCAGATTTGCCCGAGGGTTCACCAGATCCTAAACAT
GTGAAGACGTTCCATCAAAATTGTCAGGCGTATCATCAAGGGGTATGCAGAG

Alignment

ORF - retro_mmul_2571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 65.83 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IDTLHESEEGAEVLIDALVDGQVVALLVQNLERLDESVKEEADGVHNTLAIVENMAEFRPEMCTDGAQQG
          ID...ESEEGAEVLIDALVDG.V.ALLVQN.ERLDESVKEEA..VHNTL.IV.NMAEF..EMCT.GAQQG
Retrocopy IDIFYESEEGAEVLIDALVDG*VTALLVQNVERLDESVKEEANSVHNTLVIVGNMAEF*LEMCTRGAQQG

Parental  LLQWLLKRLKAKMPFDANKLYCSEVLAILLQDNDENRELLGELDGIDVLLQQLSVFKRHNPSTAEEQEMM
          L.QWLLKRLKAK.PFDANKLYCSE..AILLQDNDENR.LLGELDGID.LLQQLSVFKRHNPSTA.EQEMM
Retrocopy LPQWLLKRLKAKKPFDANKLYCSEMQAILLQDNDENRKLLGELDGIDALLQQLSVFKRHNPSTAKEQEMM

Parental  ENLFDSLCSCLMLSSNRERFLKGEGLQLMNLMLREKKISRSSALKVLDHAMIGPEGTDNCHKFVDILGLR
          EN.FDSLC..LMLSSNRE.FLKGEGLQLMNLMLREKKISRS..LKVL....I...G..NC.KFVDILGL.
Retrocopy ENPFDSLCF*LMLSSNREHFLKGEGLQLMNLMLREKKISRSRVLKVL----IASKGVYNCGKFVDILGL*

Parental  TIFPLFMKSPRKIKKVGTTEKEHEEHVCSILASLLRNLRGQQRTRLLNKFTENDSEKVDRLMELHFKYLG
          TIFPLFM..PRKIKKVGTT..EH.EHVCSILA.LL.NLRG.QRT.LLNKFTENDSE..DRLMELHF.YLG
Retrocopy TIFPLFMEFPRKIKKVGTTDREHKEHVCSILAFLLWNLRGHQRTWLLNKFTENDSE*ADRLMELHFQYLG

Parental  AMQVADKKIEGEKHDMVRRGEIIDNDIEEEFYLRRLDAGLFVLQHICYIMAEICNANVPQIRQRVHQILN
          AMQVADK..EGEKHDMV..GEIID.D...EFYL..LDAGLFVLQ.IC.IMA.ICNANVPQI..RVHQILN
Retrocopy AMQVADKRKEGEKHDMVQCGEIIDSDMGDEFYLQCLDAGLFVLQCICCIMAKICNANVPQICPRVHQILN

Parental  MRGSSIKIVRHIIKEYAE
          M...SIKIVR.IIK.YAE
Retrocopy M*RRSIKIVRRIIKGYAE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	28.12 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	33.56 RPM
SRP007412_cerebellum	0.00 RPM	28.99 RPM
SRP007412_heart	0.00 RPM	23.32 RPM
SRP007412_kidney	0.00 RPM	18.54 RPM
SRP007412_liver	0.00 RPM	16.55 RPM
SRP007412_testis	0.00 RPM	105.09 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2571 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2571 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4819
Pan troglodytes	retro_ptro_3208
Gorilla gorilla	retro_ggor_3003
Pongo abelii	retro_pabe_3747

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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,