RetrogeneDB ID: retro_mdom_149

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:269855734..269857324(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024288
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019582
• Aliases: None
• Description: None

Sequence

>retro_mdom_149
ATGGAGCACCGAATAATTGGACCCGGGCCCTACCGCGCGACTAAGCTGTGGAATGAAACAATTGAACTTTTTCGTAGTAA
CATGCCATTACGGAAACATCGAAGTCATTTCAAAAGTTATGAACGTTGCTTCACAGCCTCGGAAGCTGTAGATTGGTTAC
ATGTCCTGCTCAGGCACAGCCAGAACTTTGGCCCAGAAGTGACTCGCAAGCAGACAGTACAGCTGCTCAAAAAGTTCCTG
AAGAACCATGTTATTGAGGACATCAAGGGCAGATGGGGTCAGGAAGACTTCGAGGACAACCGACATCTCTACAGATTTCC
TCCTTCTTCACCCTTGAAACCATACCCAAAGAGATCACCCCACCAAGCAAGTGTTATCAGATTCCCAGACTGGACTCATG
AGCCACCAGGCACTAGCCAGGAGAACATACCAGTGAGGCCTATTGTTATGAATTCTGAATCATGGTACAAGCGTCACAGT
ATTGCTATCGGAGAAGTCCCTGCCTGCCGCCTCGTCTACCGGAGACAGCTGACAGAGGCCAATGTGGAAGAGATCTGGAA
GTCTATGACGTTATCGCATTTACAGAAAATCCTTGACCTGGACTCTCTGGAGGAAGTTTTGGATACCAAGCTTGTCAACT
CAAAGTTTATCATCCACAACGTATACAGTGTTAGTAAGCAGGGAGTCGTCATCCTCACGGATAAATCAAAAGAACTTCCT
CATTGGGTACTGTCAGCTATGAAATGTTTAGCAAATTGGCCTAATTGTTCAGACTTGAAGCATCCTATGTATTCAGGGTT
TGAAAAAGATGTCTTTAAAACCATAGCAGATTACTATGGTCACTTGAAGGAACCTCTGCTCACATTTCAGCTTTTTGATG
CTTTTGTCAGTGTACTTGGTTTGTTACAGAAAGAGAAAATTGCTATTGAAGCATTTCAGATTTGCTGTCTCCTCCTGCCT
CCTGAAAATCGGGGAAAGTTACAACTGTTGATTAGGATGATGGTGAAGATCTGCTTAAACAAGGAGATGCCACCACTCTG
TGATGGCCTTGGCACCCGTACTCTGATGGTTCAGACTTTTTCACGTTGCATCCTGTGCTCCAAGGATGAAGTCGATTTGG
ATGAACTATTAGCTGCCCGGCTGGTGACATTTCTGATGGACAATCACCAGGAGATCTTGCAAGCTCCCTCTTCCTTGCAG
AATTCAATAGAGGAGCGAGTGGCCCATCTACGAAGGGTCCAGATTAAATACCCAGGAGCAGATACTGATGCCACGCTGTC
TGCCCCGCCATTTTGTCGTCAGATTAGTCCAGAAGAATTTGAATACCAAAGAGTATGTGGCTCCCAAGAACCCCTGGAAA
AATTGTTGGAGGAAATTATCATGGATTCCAAACTGTCAGTTAAGGATAAAAAGAAAAAACTGAAACAGTTTCAGAAATCT
TATCCTGAAGTCTACCAGGAACGGTTTCCCACACCAGAGAGTGAAGCGTTGATTTTTCCAGAAAAATCAAAGCCAAAACC
ACAGCTGCTGATGTGGGCACTGAAAAAACCTTTCCAGCCTTTTCAAAGAACTAGAAGTTTTCGGATGTAA

Alignment

ORF - retro_mdom_149 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEHRIIGPGPYRATKLWNETIELFRSNMPLRKHRSHFKSYERCFTASEAVDWLHVLLRHSQNFGPEVTRK
          MEHRIIGPGPYRATKLWNETIELFRSNMPLRKHRSHFKSYERCFTASEAVDWLHVLLRHSQNFGPEVTRK
Retrocopy MEHRIIGPGPYRATKLWNETIELFRSNMPLRKHRSHFKSYERCFTASEAVDWLHVLLRHSQNFGPEVTRK

Parental  QTVQLLKKFLKNHVIEDIKGRWGQEDFEDNRHLYRFPPSSPLKPYPKRSPHQASVIRFPDWTHEPPGTSQ
          QTVQLLKKFLKNHVIEDIKGRWGQEDFEDNRHLYRFPPSSPLKPYPKRSPHQASVIRFPDWTHEPPGTSQ
Retrocopy QTVQLLKKFLKNHVIEDIKGRWGQEDFEDNRHLYRFPPSSPLKPYPKRSPHQASVIRFPDWTHEPPGTSQ

Parental  ENIPVRPIVMNSESWYKRHSIAIGEVPACRLVYRRQLTEANVEEIWKSMTLSHLQKILDLDSLEEVLDTK
          ENIPVRPIVMNSESWYKRHSIAIGEVPACRLVYRRQLTEANVEEIWKSMTLSHLQKILDLDSLEEVLDTK
Retrocopy ENIPVRPIVMNSESWYKRHSIAIGEVPACRLVYRRQLTEANVEEIWKSMTLSHLQKILDLDSLEEVLDTK

Parental  LVNSKFIIHNVYSVSKQGVVILTDKSKELPHWVLSAMKCLANWPNCSDLKHPMYSGFEKDVFKTIADYYG
          LVNSKFIIHNVYSVSKQGVVILTDKSKELPHWVLSAMKCLANWPNCSDLKHPMYSGFEKDVFKTIADYYG
Retrocopy LVNSKFIIHNVYSVSKQGVVILTDKSKELPHWVLSAMKCLANWPNCSDLKHPMYSGFEKDVFKTIADYYG

Parental  HLKEPLLTFQLFDAFVSVLGLLQKEKIAIEAFQICCLLLPPENRRKLQLLIRMMVKICLNKEMPPLCDGL
          HLKEPLLTFQLFDAFVSVLGLLQKEKIAIEAFQICCLLLPPENR.KLQLLIRMMVKICLNKEMPPLCDGL
Retrocopy HLKEPLLTFQLFDAFVSVLGLLQKEKIAIEAFQICCLLLPPENRGKLQLLIRMMVKICLNKEMPPLCDGL

Parental  GTRTLMVQTFSRCILCSKDEVDLDELLAARLVTFLMDNHQEILQAPSSLQNSIEERVAHLRRVQIKYPGA
          GTRTLMVQTFSRCILCSKDEVDLDELLAARLVTFLMDNHQEILQAPSSLQNSIEERVAHLRRVQIKYPGA
Retrocopy GTRTLMVQTFSRCILCSKDEVDLDELLAARLVTFLMDNHQEILQAPSSLQNSIEERVAHLRRVQIKYPGA

Parental  DTDATLSAPPFCRQISPEEFEYQRVCGSQEPLEKLLEEIIMDSKLSVKDKKKKLKQFQKSYPEVYQERFP
          DTDATLSAPPFCRQISPEEFEYQRVCGSQEPLEKLLEEIIMDSKLSVKDKKKKLKQFQKSYPEVYQERFP
Retrocopy DTDATLSAPPFCRQISPEEFEYQRVCGSQEPLEKLLEEIIMDSKLSVKDKKKKLKQFQKSYPEVYQERFP

Parental  TPESEALIFPEKSKPKPQLLMWALKKPFQPFQRTRSFRM
          TPESEALIFPEKSKPKPQLLMWALKKPFQPFQRTRSFRM
Retrocopy TPESEALIFPEKSKPKPQLLMWALKKPFQPFQRTRSFRM

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_149 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_149 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009718	1 retrocopy	retro_mdom_1180,
Monodelphis domestica	ENSMODG00000019582	1 retrocopy	retro_mdom_149 ,