RetrogeneDB ID: retro_mmul_2019

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:75566001..75566582(+)
• Located in intron of: ENSMMUG00000029972

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2015
• Ensembl ID: ENSMMUG00000013980
• Aliases: None
• Description: methionine adenosyltransferase 2 subunit beta [Source:RefSeq peptide;Acc:NP_001244402]

Sequence

>retro_mmul_2019
ATGGTGGGGCGGGAGAAAGAGCTCTCTATACACTTTGTTCCCAGGAGCTGCCGGCTGGTGGAGGAGGAAGTTAACATCCC
TAATAGGAGGGTTCTGGTTACTGGTGCCACTGGGCTTCTTGGCAGAGCTGTACACAAACAATTTCAGCAGAATAATTGGC
ATGCTGTTGGCTGTGGTTTTAGAAGAGCAAGACCAAAATTTGACCAGGTTAATCTGTGGATTCTAATGCAGTTCATCACA
TCATTCATGATTTTCAGCCCCATGTTATAGTGCATTGTGCAGCAGAGAGAAGACCAGATGTTGTAGAAAATCAGCCAGAT
GCTGCCTCTCAACTTAATGTGGATGCTTCTGGGAATTTAGCAAAGGAAGCAGCTGCTGTTGGGGCATTTCTCATCTACAT
TAGCTCAGATTATGTATTTGATGGAACAAATCCACCTTACAGAGAGGAAGACATACCAGCTCCCCTAAATTTGTATGGCA
AAACAAAATTAGATGGAGAAAAGGCTGTCCTGGAGAACACTTTAGGAGCTGCTGTTTTGAGGATTCCTATTCTGTATGGG
GAAGTTGAAAAGCTCGAAGAA

Alignment

ORF - retro_mmul_2019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.92 %
• Parental protein coverage: 58.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVGREKELSIHFVPGSCRLVEEEVNIPNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQV
          MVGREKELSIHFVP.SCRLVEEEVNIPNRRVLVTGATGLLGRAVHK.FQQNNWHAVGCGFRRARPKF.QV
Retrocopy MVGREKELSIHFVPRSCRLVEEEVNIPNRRVLVTGATGLLGRAVHKQFQQNNWHAVGCGFRRARPKFDQV

Parental  NL-LDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYV
          NL..DSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYV
Retrocopy NL<VDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYV

Parental  FDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEE
          FDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLEN.LGAAVLRIPILYGEVEKLEE
Retrocopy FDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENTLGAAVLRIPILYGEVEKLEE

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	38.77 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	42.44 RPM
SRP007412_cerebellum	0.13 RPM	38.42 RPM
SRP007412_heart	0.00 RPM	33.62 RPM
SRP007412_kidney	0.00 RPM	46.13 RPM
SRP007412_liver	0.00 RPM	20.70 RPM
SRP007412_testis	0.00 RPM	18.13 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2019 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2019 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2019 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012350	1 retrocopy	retro_btau_387,
Callithrix jacchus	ENSCJAG00000015401	1 retrocopy	retro_cjac_1749,
Macaca mulatta	ENSMMUG00000013980	1 retrocopy	retro_mmul_2019 ,
Ictidomys tridecemlineatus	ENSSTOG00000009459	1 retrocopy	retro_itri_1696,
Tursiops truncatus	ENSTTRG00000001154	1 retrocopy	retro_ttru_1573,