RetrogeneDB ID: retro_mdom_200

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:154588322..154588913(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024615
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010588
• Aliases: None
• Description: None

Sequence

>retro_mdom_200
TTGTCCTTGCAAGCCTTGAGTACCCAACTCGATCTTTGCCTCCTGCGGCTATTCGTGGAGCTCGAGGAGCTGGAAGGAAA
GCGGAAAGCCTTGAACGCCCGAGTGGAGGAGGGCTGGTTTTCCCTGTCCAAGACTCGTTACGCCATGGGCGCCAAGGCCG
TGAGCTCCCTTCAGTATGCTTCCTCAATGGTTCCTCTCTTCCGGGTCTGCATCAGTGAGCTCGAGACCGGTCGGCCTGAG
TTCCAGGTGGTGTTCACTGACCCCAAGGAAGCCCAAGATGTGACTGATTATGAGGATCCCAAGTCGGAGGCTCCATTAAC
TCCTGTGCTTCGGCGTCGACCTCAGCACCACGGGTCTCCTTTGCAGTCCACCCCACCAGCTGCCCCCTGGGCATCTCCTG
ATCGAGATCCGTTGACTTGGTTTGGTATCTTGGTGCCCCAGAGTCTACGGCAAGCCCAGGGAAGTTTCCGCGGAGCCCTG
CAGATTGCTGGGGAGATTGCTGAGCTCCAGGGCCGAATCGAGTGGTGTAGAACTCAGGTTCAAGCCCTGCAAAAGGAGAA
ACAAAAACTGCTTGAACAGCTGAAGGTCTGA

Alignment

ORF - retro_mdom_200 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.15 %
• Parental protein coverage: 85.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALPTLNAELDALLLQLLLDLEHLEGKRAALNARVEEGWLSLSKSRYAMGVKAVGPLQYGSSMAALFRVGI
          .L..L...LD..LL.L...LE.LEGKR.ALNARVEEGW.SLSK.RYAMG.KAV..LQY.SSM..LFRV.I
Retrocopy SLQALSTQLDLCLLRLFVELEELEGKRKALNARVEEGWFSLSKTRYAMGAKAVSSLQYASSMVPLFRVCI

Parental  SEPEPGRPEFQVMFTDPKEAQGLM---EPKAEVPFPPVRRRRTQ----PQPTCPEPAPLALPKRDPLTWF
          SE.E.GRPEFQV.FTDPKEAQ.......PK.E.P..PV.RRR.Q....P....P..AP.A.P.RDPLTWF
Retrocopy SELETGRPEFQVVFTDPKEAQDVTDYEDPKSEAPLTPVLRRRPQHHGSPLQSTPPAAPWASPDRDPLTWF

Parental  GILVPQSLRQAQGSFRAALLMAGEVAGLQSRIEWGRGQIQILLQEKRKLLDQLKV
          GILVPQSLRQAQGSFR.AL..AGE.A.LQ.RIEW.R.Q.Q.L..EK.KLL.QLKV
Retrocopy GILVPQSLRQAQGSFRGALQIAGEIAELQGRIEWCRTQVQALQKEKQKLLEQLKV

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_200 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_200 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010588	2 retrocopies	retro_mdom_200 , retro_mdom_435,
Mus musculus	ENSMUSG00000042111	2 retrocopies	retro_mmus_2696, retro_mmus_380,
Oryctolagus cuniculus	ENSOCUG00000005099	1 retrocopy	retro_ocun_1651,
Otolemur garnettii	ENSOGAG00000000166	2 retrocopies	retro_ogar_2849, retro_ogar_3466,
Tursiops truncatus	ENSTTRG00000012598	1 retrocopy	retro_ttru_781,