RetrogeneDB ID: retro_mdom_103

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:714139916..714141050(-)
• Located in intron of: ENSMODG00000023052

Retrocopy information

• Ensembl ID: ENSMODG00000011849
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001048
• Aliases: None
• Description: None

Sequence

>retro_mdom_103
ATGGCGGGGTCTAGCAGCCTGTGGGGCACAGAGCCGCCCCACTTCCTGGAGGCCTTCGGACGACTCTGGCAGGTACAGAG
CTGGCTGGGCAGCGGCTCCTCGGCCTCTGTGTACTGGGTACGATGCTGCGGGACTCCTGGATCGCCACCTGGGGCCCTCA
AACAATTCCTACCACCCGGGACCACTGCCATAGCCTCGGCCACCGAATACGGCTTTCATAAGGAGAGGGCAGTGCTGGAA
CAGTTACAAGGCCACCGAAACATCATGACCCTGTATGGAGTATTTACTATCCAATTTCCTCCAAATATGCCATCATACTG
TCTACTTCTTGAACTACTGGATGTCAGTGTTTTGGAACTGCTTTTATATTCTAGTCATCAAGGGTGTTCCATGTGGATGA
TCCAACACTGTGCCAGAGGTGTTTTAGAGGCCCTGGCTTTTCTTCACCATGAGGGCTATGTTCATGCAGACCTAAAGTCA
TGTAACATACTGTGGAGTGCAGAGAATGAATGCTTTAAACTTATTGACTTTGGTCTTAGCTTCAAGGAAGGCAATCAGGA
TGTAAAGTATATCCAGACAGACAGGTATCAGGCTCCAGAAGCAGAAATACAGAATTGTTTGGCCCAGGCTGGGCTACAGA
GTGAAACAGAATGTACCTCAGCTGTTGATTTGTGGAGCCTCGGAATCATCTTGCTGGAAATGTTCTCAGGAATGAAACTG
AAACATATGATCAGATCTCAGGAATGGAAGGTAAACAGTTCAGCTATCATTGATCACATATTTGCCAGTAAAGCTGTGGT
GACCTCTGCAATCCCAGCCTATCACCTCAGAGACCTTATCAAAAGCATGCTTCATGATGACCCAAGCAGAAGAATTCCAG
CTGATATGGCGCTCTGTAGTCCCTTCTTTAGCATTCCTTTTGCCCCTCATATTGAAGATTTGGTGATGCTTCCTACGCCT
GTGCTAAGATTGTTCAATGTATTGGATGATGACTATCTTGAGAATGAGGAAGAATATGAAGATGTTGTAGAAGATGTGAA
AGAAGAGTGTCAGAAGTATGGGCCAGTGGTGTCTCTGCTTGTTCCAAAGGAGAACCCAGGCAGAGGTCAGGTCTTTGTTG
AATATGCAAATGCA

Alignment

ORF - retro_mdom_103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.93 %
• Parental protein coverage: 96.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGSGCLWGAEPPRFLEAFGRLWQVQSRLGSGSSASVYRVRCCGTPGSPPGALKQFLPPGTTGAAASAAE
          MAGS..LWG.EPP.FLEAFGRLWQVQS.LGSGSSASVY.VRCCGTPGSPPGALKQFLPPGTT.A.ASA.E
Retrocopy MAGSSSLWGTEPPHFLEAFGRLWQVQSWLGSGSSASVYWVRCCGTPGSPPGALKQFLPPGTT-AIASATE

Parental  YGFRKERAALEQLQGHRNIVTLYGVFTIQFSPNMPSRCLLLELLDVSVSELLLYSSHQGCSMWMIQHCAR
          YGF.KERA.LEQLQGHRNI.TLYGVFTIQF.PNMPS.CLLLELLDVSV.ELLLYSSHQGCSMWMIQHCAR
Retrocopy YGFHKERAVLEQLQGHRNIMTLYGVFTIQFPPNMPSYCLLLELLDVSVLELLLYSSHQGCSMWMIQHCAR

Parental  DVLEALAFLHHEGYVHADLKPRNILWSAENECFKLIDFGLSFKEGNQDVKYIQTDGYRAPEAEIQNCLAQ
          .VLEALAFLHHEGYVHADLK..NILWSAENECFKLIDFGLSFKEGNQDVKYIQTD.Y.APEAEIQNCLAQ
Retrocopy GVLEALAFLHHEGYVHADLKSCNILWSAENECFKLIDFGLSFKEGNQDVKYIQTDRYQAPEAEIQNCLAQ

Parental  AGLQSETECTSAVDLWSLGIILLEMFSGMKLKHTIRSQEWKVNSSAIIDHIFASKAVVTSAIPAYHLRDL
          AGLQSETECTSAVDLWSLGIILLEMFSGMKLKH.IRSQEWKVNSSAIIDHIFASKAVVTSAIPAYHLRDL
Retrocopy AGLQSETECTSAVDLWSLGIILLEMFSGMKLKHMIRSQEWKVNSSAIIDHIFASKAVVTSAIPAYHLRDL

Parental  IKSMLHDDPGRRIPADMALCSPFFSIPFAPHIEDLVMLPTPVLRLLNVLDDDYLENEEEYEDVVEDVKEE
          IKSMLHDDP.RRIPADMALCSPFFSIPFAPHIEDLVMLPTPVLRL.NVLDDDYLENEEEYEDVVEDVKEE
Retrocopy IKSMLHDDPSRRIPADMALCSPFFSIPFAPHIEDLVMLPTPVLRLFNVLDDDYLENEEEYEDVVEDVKEE

Parental  CQKYGPVVSLLVPKENPGRGQVFVEYANA
          CQKYGPVVSLLVPKENPGRGQVFVEYANA
Retrocopy CQKYGPVVSLLVPKENPGRGQVFVEYANA

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_103 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_103 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001048	1 retrocopy	retro_mdom_103 ,
Oryctolagus cuniculus	ENSOCUG00000012411	3 retrocopies	retro_ocun_1245, retro_ocun_1535, retro_ocun_1547,
Rattus norvegicus	ENSRNOG00000002941	1 retrocopy	retro_rnor_1274,