RetrogeneDB ID: retro_mdom_372

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:304522258..304522666(+)
• Located in intron of: ENSMODG00000014139

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TP53
• Ensembl ID: ENSMODG00000007271
• Aliases: None
• Description: tumor protein p53 [Source:HGNC Symbol;Acc:11998]

Sequence

>retro_mdom_372
GATTCCAGGAGTCAACTTCTTGGACATTGAAACTTTGAAGTATGCATATGTGCCTGCCCTGGAAGAGACTGGCGGACTGA
AGAGGGAAATCTCCACAAGAAGGGAGATCCCAGTGCACAGACATCATCTGAGAACAATAATAGTGCATTGCCCACAACCC
CTGGTAGCACCCCCAAGGCCAAAAAGAAGCCAGTGGAAGGAGAATATTTCACTCTTCAGATCTGAGGTCGACAGTGCTAT
TAACTGCTTCAGGAGATAAATGAAGCCTTGGAGCTGAAAGAAGCTCACAACAGGAAAGAACCTGAGGGGAGCCGCCCCCA
CCGCAGCCAACTGAAGTACAAGAGAGGAGATTCTACCACCTGTCGAGGCTGAAGACTTTTGGTGAAAAATGAAGTTCCTG
ACTGTGAA

Alignment

ORF - retro_mdom_372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.88 %
• Parental protein coverage: 90.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DSRGQLLGRRSFEVRICACPGRDRRTEEENFHKKGGPSPQPSSESNKRALPTTPGSTPKAKKKLVEGEYF
          DSR.QLLG...FEV.ICACPGRD.RTEE.N.HKKG.PS.Q.SSE.N..ALPTTPGSTPKAKKK.VEGEYF
Retrocopy DSRSQLLGH*NFEVCICACPGRDWRTEEGNLHKKGDPSAQTSSENNNSALPTTPGSTPKAKKKPVEGEYF

Parental  TLQIRGRQRYELLREINEALELKEAHSRKEPEGSRPHRSQLKSKRGDSTPCQGKRLLVKNEVPDSD
          TLQI.GRQ.Y.LL.EINEALELKEAH.RKEPEGSRPHRSQLK.KRGDST.C.G.RLLVKNEVPD..
Retrocopy TLQI*GRQCY*LLQEINEALELKEAHNRKEPEGSRPHRSQLKYKRGDSTTCRG*RLLVKNEVPDCE

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	0.12 RPM	0.00 RPM
SRP007412_cerebellum	0.98 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	1.32 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_372 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_372 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
Macropus eugenii	ENSMEUG00000013135	2 retrocopies	retro_meug_1464, retro_meug_599,
Myotis lucifugus	ENSMLUG00000006411	3 retrocopies	retro_mluc_2049, retro_mluc_2050, retro_mluc_452,
Monodelphis domestica	ENSMODG00000007271	1 retrocopy	retro_mdom_372 ,
Rattus norvegicus	ENSRNOG00000010756	1 retrocopy	retro_rnor_1411,
Sarcophilus harrisii	ENSSHAG00000015510	1 retrocopy	retro_shar_250,