RetrogeneDB ID: retro_mdom_1984

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:65379104..65379927(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000008274
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRKAB1
• Ensembl ID: ENSMODG00000015269
• Aliases: None
• Description: protein kinase, AMP-activated, beta 1 non-catalytic subunit [Source:HGNC Symbol;Acc:9378]

Sequence

>retro_mdom_1984
ATGGGTAACACAAGCAGTGAGCCGGCTGGGATGGAGCGCCAGGGAGGCCACAAGACAACCGGGAGGGATAGTTCTGGGGG
AGCCATCACGACCAAAGATGGGGACAGGCCCAAGATCTTGATGGACAGCCCCGAGGATGCTGACCTCTTCCACTCTGAAG
AGATCAAGGCTCCAGAAAAGGAAGAATTCCTTGTGTGGCAGCATGATCTGGAAGTAAATGACAGAGCTCCCACCCAGGCT
CGTCCAACTGTGTTTCGCTGGACAGGGGGAGGAAAAGAGGTTTACTTATCTGGATCCTTCAATAACTGGACTAAACTTCC
CCTCACAAGAAGCCACAACAACTTTGTAGCTATACTGGATTTGCCAGAAGGAGAGCATCAGTACAAGTTCTATGTGGATG
GTCAGTGGACCTATGATCCCTCTGAGCCAGTAGTGACCAGCCAGCTTGGCACAGTCAACAATGTCATTCAGGTGAAGAAG
ACTGACTTTGAAGTGTTTGATGCTTTAATGGTGGATTCCCAAAAGTGCTCCGATGTTTCAGAGCTTTCAAGTTCACCACC
AGGACTCTACCATCAGGAGACTTGTGTTTGTAAGCCAGAGGAATGTTTCAAAACTCCACCCATCCTTCCCCCACACCTGC
TCCAGGTCATCCTCAATAAGGACACTGGCATCTCATGTGACCGACCCAGTTTTGCTCCCCGAGCCCAACCACATCATGCT
GAACCACCTGTATGCCCTCTCCATCAAGGACGGCATGATGGTGCTCAGTGCCACCCACCACTACAAGAAGAAATACGTCA
CCACCTTGCTGTACAAGCCCATA

Alignment

ORF - retro_mdom_1984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGNTSSERAGMERQGGHKTARRDSSGGAITTKDGDRPKILMDSPEDADLFHSEEIKAPEKEEFLAWQHDL
          MGNTSSE.AGMERQGGHKT..RDSSGGAITTKDGDRPKILMDSPEDADLFHSEEIKAPEKEEFL.WQHDL
Retrocopy MGNTSSEPAGMERQGGHKTTGRDSSGGAITTKDGDRPKILMDSPEDADLFHSEEIKAPEKEEFLVWQHDL

Parental  EVNDRAPTQARPTVFRWTGGGKEVYLSGSFNNWTKLPLTRSHNNFVAILDLPEGEHQYKFYVDGQWTYDP
          EVNDRAPTQARPTVFRWTGGGKEVYLSGSFNNWTKLPLTRSHNNFVAILDLPEGEHQYKFYVDGQWTYDP
Retrocopy EVNDRAPTQARPTVFRWTGGGKEVYLSGSFNNWTKLPLTRSHNNFVAILDLPEGEHQYKFYVDGQWTYDP

Parental  SEPVVTSQLGTVNNVIQVKKTDFEVFDALMVDSQKCSDVSGRKPLSSSPPGPYHQEPYVCKPEERFKTPP
          SEPVVTSQLGTVNNVIQVKKTDFEVFDALMVDSQKCSDVS....LSSSPPG.YHQE..VCKPEE.FKTPP
Retrocopy SEPVVTSQLGTVNNVIQVKKTDFEVFDALMVDSQKCSDVS---ELSSSPPGLYHQETCVCKPEECFKTPP

Parental  ILPPHLLQVILNKDTGISCD-PA-LLPEPNHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI
          ILPPHLLQVILNKDTGISCD.P..LLPEPNH.MLNHLYALSIKDG.MVLSATH.YKKKYVTTLLYKPI
Retrocopy ILPPHLLQVILNKDTGISCDRPS>LLPEPNHIMLNHLYALSIKDGMMVLSATHHYKKKYVTTLLYKPI

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1984 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1984 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
Macropus eugenii	ENSMEUG00000006584	1 retrocopy	retro_meug_2055,
Monodelphis domestica	ENSMODG00000015269	1 retrocopy	retro_mdom_1984 ,
Ictidomys tridecemlineatus	ENSSTOG00000008615	1 retrocopy	retro_itri_1535,