RetrogeneDB ID: retro_mdom_78

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:567736679..567738440(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005722
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000007642
• Aliases: None
• Description: None

Sequence

>retro_mdom_78
ATGCCGAAGCCAATCAATGTCCGTGTTACCACCATGGATGCAGAACTGGAGTTTGCCATCCAGCCCAATACCACTGGAAA
GCAACTCTTTGACCAGGTGGTTAAGACCATTGGCCTTCGGGAAGTGTGGTACTTTGGCCTCCAATATGTGGATAATAAAG
GATTTCCAACCTGGTTGAAGCTTGATAAAAAGGTCTCTGCTCAGGAGGTCAGAAAGGAGAGCCCCCTCCAGTTCAAATTC
CGGGCCAAGTTCTACCCAGAGGATGTGCCTGAGGAGCTGATCCAGGACATCACCCAGAAGTTGTTCTTCCTACAAGTGAA
AGATGGAATCCTAAGTGATGAAATCTACTGCCCGCCCGAGACGGCTGTGCTCCTGGGCTCCTACGCCGTCCAAGCCAAGT
TTGGAGATTATAATAAAGAGGTGCACAAGTCCGGCTACCTTGGCTCTGAACGTTTGATCCCTCAAAGAGTAATGGACCAA
CACAAGCTCTCCAGAGAACAGTGGGAGGACCGGATCCAGGTGTGGCATGCTGAACACCGTGGGATGCTTAAAGATAATGC
CATGCTGGAATATCTGAAGATTGCTCAAGACTTGGAGATGTATGGGATCAATTATTTTGAGATAAAAAACAAAAAAGGAA
CAGACCTTTGGCTTGGAGTGGATGCCCTGGGGCTGAATATTTATGAGAAAGATGATAAATTGACCCCCAAAATTGGCTTC
CCTTGGAGTGAAATCAGGAACATCTCTTTCAATGACAAAAAGTTTGTCATCAAACCCATCGACAAGAAGGCACCTGACTT
TGTATTTTATGCTCCTCGCCTCCGGATTAATAAGCGGATCCTTCAGCTTTGCATGGGGAACCATGAGCTCTACATGCGCC
GTAGGAAGCCAGATACCATCGAGGTACAACAGATGAAAGCCCAGGCACGGGAAGAGAAGCACCAGAAACAGCTGGAGAGG
CAGCAGTTGGAGACTGAAAAAAAGAGAAGAGAGACTGTGGAACGAGAGAAGGAGCAGATGCTGAGAGAGAAGGAGGAACT
GATGATGAGGCTTCAGGACTATGAACAGAAGACCAAGAAAGCAGAAAAGGAGCTCTCAGATCAGATCCAGAGGGCTATTC
AACTGGAAGAAGAGAGGAAGAGAGCCCAGGAAGAGGCTGAGCGTCTTGAGGCCGACCGTGTGGCTGCTCTCCGAGCCAAG
GAGGAACTGGAGAGACAGGCTGTAGATCAGATAAAGAGCCAGGAGCAGCTGGCTGCTGAACTTGCTGAATACACCGCCAA
GATTGCTCTCCTGGAAGAGGCAAGGAGGCGTAAGGAGGATGAAGTCGAAGAATGGCAGATCAGGGCCAGGGAAGCCCAAG
ATGATCTTGTCAAGACCAAGGAAGAGCTTCACCAGGTGATGACCGCCCCTCCACCACCCCCACCTCCTGTGTACGAGCCT
GTGAATTACCACGTGCATGAGAACCTACAGGACGAAGGGACTGAATACAGCGGCTACAGCGCCGAGTTCTCCAGCGAGGG
CATCATGGATGACCGAAATGAAGAAAAACGAATCACTGAGGCTGAGAAGAATGAGCGTGTGCAGAGACAGCTGCAGACAC
TGACAAATGAGCTGTCCCAGGCCAGGGATGAGAATAAGAGGACCCACAATGACATCATCCACAACGAGAACATGAGACAA
GGACGGGACAAGTACAAGACTCTGAGACAGATTCGACAGGGGAACACAAAGCAGAGAATCGATGAGTTTGAAGCTATGTA
A

Alignment

ORF - retro_mdom_78 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKPINVRVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWYFGLQYVDNKGFPTWLKLDKKVSAQEV
          MPKPINVRVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWYFGLQYVDNKGFPTWLKLDKKVSAQEV
Retrocopy MPKPINVRVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWYFGLQYVDNKGFPTWLKLDKKVSAQEV

Parental  RKESPLQFKFRAKFYPEDVPEELIQDITQKLFFLQVKDGILSDEIYCPPETAVLLGSYAVQAKFGDYNKE
          RKESPLQFKFRAKFYPEDVPEELIQDITQKLFFLQVKDGILSDEIYCPPETAVLLGSYAVQAKFGDYNKE
Retrocopy RKESPLQFKFRAKFYPEDVPEELIQDITQKLFFLQVKDGILSDEIYCPPETAVLLGSYAVQAKFGDYNKE

Parental  VHKSGYLGSERLIPQRVMDQHKLSREQWEDRIQVWHAEHRGMLKDNAMLEYLKIAQDLEMYGINYFEIKN
          VHKSGYLGSERLIPQRVMDQHKLSREQWEDRIQVWHAEHRGMLKDNAMLEYLKIAQDLEMYGINYFEIKN
Retrocopy VHKSGYLGSERLIPQRVMDQHKLSREQWEDRIQVWHAEHRGMLKDNAMLEYLKIAQDLEMYGINYFEIKN

Parental  KKGTDLWLGVDALGLNIYEKDDKLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKRI
          KKGTDLWLGVDALGLNIYEKDDKLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKRI
Retrocopy KKGTDLWLGVDALGLNIYEKDDKLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKRI

Parental  LQLCMGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQLERQQLETEKKRRETVEREKEQMLREKEELMMR
          LQLCMGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQLERQQLETEKKRRETVEREKEQMLREKEELMMR
Retrocopy LQLCMGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQLERQQLETEKKRRETVEREKEQMLREKEELMMR

Parental  LQDYEQKTKKAEKELSDQIQRAIQLEEERKRAQEEAERLEADRVAALRAKEELERQAVDQIKSQEQLAAE
          LQDYEQKTKKAEKELSDQIQRAIQLEEERKRAQEEAERLEADRVAALRAKEELERQAVDQIKSQEQLAAE
Retrocopy LQDYEQKTKKAEKELSDQIQRAIQLEEERKRAQEEAERLEADRVAALRAKEELERQAVDQIKSQEQLAAE

Parental  LAEYTAKIALLEEARRRKEDEVEEWQIRAREAQDDLVKTKEELHQVMTAPPPPPPPVYEPVNYHVHENLQ
          LAEYTAKIALLEEARRRKEDEVEEWQIRAREAQDDLVKTKEELHQVMTAPPPPPPPVYEPVNYHVHENLQ
Retrocopy LAEYTAKIALLEEARRRKEDEVEEWQIRAREAQDDLVKTKEELHQVMTAPPPPPPPVYEPVNYHVHENLQ

Parental  DEGTEYSGYSAEFSSEGIMDDRNEEKRITEAEKNERVQRQLQTLTNELSQARDENKRTHNDIIHNENMRQ
          DEGTEYSGYSAEFSSEGIMDDRNEEKRITEAEKNERVQRQLQTLTNELSQARDENKRTHNDIIHNENMRQ
Retrocopy DEGTEYSGYSAEFSSEGIMDDRNEEKRITEAEKNERVQRQLQTLTNELSQARDENKRTHNDIIHNENMRQ

Parental  GRDKYKTLRQIRQGNTKQRIDEFEAM
          GRDKYKTLRQIRQGNTKQRIDEFEAM
Retrocopy GRDKYKTLRQIRQGNTKQRIDEFEAM

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	22.89 RPM	0.00 RPM
SRP007412_cerebellum	16.98 RPM	0.00 RPM
SRP007412_heart	15.15 RPM	0.00 RPM
SRP007412_kidney	317.36 RPM	0.00 RPM
SRP007412_liver	15.10 RPM	0.00 RPM
SRP007412_testis	3.14 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_78 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_78 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
Gorilla gorilla	ENSGGOG00000013301	1 retrocopy	retro_ggor_690,
Myotis lucifugus	ENSMLUG00000001931	3 retrocopies	retro_mluc_2037, retro_mluc_358, retro_mluc_469,
Monodelphis domestica	ENSMODG00000007642	1 retrocopy	retro_mdom_78 ,