RetrogeneDB ID: retro_mdom_529

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:179679292..179680354(-)
• Located in intron of: ENSMODG00000002423

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R2A
• Ensembl ID: ENSMODG00000016691
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B, alpha [Source:HGNC Symbol;Acc:9304]

Sequence

>retro_mdom_529
ATGGCAGGAGCTTGAGAAGGAAATGATATTCAGTGGTGTTTTTCTCAGGTGAAAGGGGCAGTCAATGATGATGTAGCAGA
AGCAGATATAATTTCTACAGTAGAATTTAACCATTCTGGAGAATTGCTAGCAACAGGAGATAAAGGAGGTAGAGTCGTCA
TCTTCCAACAGGAGCAGGAGAACAAAACCCAAACACATAGTAGAGGAGAATACAATGTTTACAGCACCTTCCAGAGCCAT
GAACCTGAGTTTCACTACTTGAAAAGTTTAGAAATTGAAGAAAAGATCAACAAAATTAGGTGGTTGCCTCAGAAAAATGC
TGCTCAGTTTTTATTATCTACCAATGATAAAACAATAAAGTTATGGAAAATATCTGAAAGGGACAAAAGACCAAAGGGAT
ATCATTTAAAGGAAGAAGATGGTTGATATAGGGATCCTACAACAGTTACTAAACTACAGGTGCCAGTATTTAGGCCCATG
GATCTGATGGTTGAGGCAAGTCCAAGGAGAATATTTGCCAATGCACATACATATCACATCAACTCTATCTCTATCAATAG
TGATTATGAAACATATCTATCTGCAGATGATTTGCGGATTAATCTTTGGAACCTTGAGATTATGGACAGAAATTTTAATA
TTGTAGATATCAAACCTGCCAACATGGAAGAGCTGACAGAGGTCATCATGGCAGCAGAGTTCTATCCCAACAGTTGTAAC
ACATCCGTGTACAGCATCAGTAAAGGCACAATTCGATGGTGTGACATGAGGGTGTCTGCACTTTGTGACTGGCATTCTAA
ATTGTTTGAGGAACCTGAAGATCCCAGTAACAGATACTTTTTCTCTGAAATCATTTCGTCCATTTCTGATGTAAAATTCA
GCTACAGTGGGCGATATATGATGACTAGAAATTACCTGTCAGTAAAAATCTGGGATTTAAACATGGAAAACAGACCTGTG
GAAACCTACCAGGTGCATGAATACCTCAGAAGTAAACTTTGCTCGCTGTATGAGAATGACTGCATTTTTGACAAATTTGA
GTGTTGTTGGAATGGATCTGAC

Alignment

ORF - retro_mdom_529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 79.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLGAGGGNDIQWCFSQVKGAVDDDVAEADIISTVEFNHSGELLATGDKGGRVVIFQQEQENKTQTHSRGE
          ..GA..GNDIQWCFSQVKGAV.DDVAEADIISTVEFNHSGELLATGDKGGRVVIFQQEQENKTQTHSRGE
Retrocopy MAGA*EGNDIQWCFSQVKGAVNDDVAEADIISTVEFNHSGELLATGDKGGRVVIFQQEQENKTQTHSRGE

Parental  YNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLPQKNAAQFLLSTNDKTIKLWKISERDKRPEGYNLKEED
          YNVYSTFQSHEPEF.YLKSLEIEEKINKIRWLPQKNAAQFLLSTNDKTIKLWKISERDKRP.GY.LKEED
Retrocopy YNVYSTFQSHEPEFHYLKSLEIEEKINKIRWLPQKNAAQFLLSTNDKTIKLWKISERDKRPKGYHLKEED

Parental  GRYRDPTTVTTLRVPVFRPMDLMVEASPRRIFANAHTYHINSISINSDYETYLSADDLRINLWHLEITDR
          G.YRDPTTVT.L.VPVFRPMDLMVEASPRRIFANAHTYHINSISINSDYETYLSADDLRINLW.LEI.DR
Retrocopy G*YRDPTTVTKLQVPVFRPMDLMVEASPRRIFANAHTYHINSISINSDYETYLSADDLRINLWNLEIMDR

Parental  SFNIVDIKPANMEELTEVITAAEFHPNSCNTFVYSSSKGTIRLCDMRASALCDRHSKLFEEPEDPSNRSF
          .FNIVDIKPANMEELTEVI.AAEF.PNSCNT.VYS.SKGTIR.CDMR.SALCD.HSKLFEEPEDPSNR.F
Retrocopy NFNIVDIKPANMEELTEVIMAAEFYPNSCNTSVYSISKGTIRWCDMRVSALCDWHSKLFEEPEDPSNRYF

Parental  FSEIISSISDVKFSHSGRYMMTRDYLSVKIWDLNMENRPVETYQVHEYLRSKLCSLYENDCIFDKFECCW
          FSEIISSISDVKFS.SGRYMMTR.YLSVKIWDLNMENRPVETYQVHEYLRSKLCSLYENDCIFDKFECCW
Retrocopy FSEIISSISDVKFSYSGRYMMTRNYLSVKIWDLNMENRPVETYQVHEYLRSKLCSLYENDCIFDKFECCW

Parental  NGSD
          NGSD
Retrocopy NGSD

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	0.72 RPM	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	1.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	1.01 RPM	0.00 RPM
SRP007412_testis	1.57 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_529 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_529 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019205	1 retrocopy	retro_ecab_305,
Monodelphis domestica	ENSMODG00000016691	1 retrocopy	retro_mdom_529 ,
Mus musculus	ENSMUSG00000022052	1 retrocopy	retro_mmus_874,