RetrogeneDB ID: retro_mdom_1587

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:60864163..60864550(+)
• Located in intron of: ENSMODG00000007266

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000028765
• Aliases: None
• Description: None

Sequence

>retro_mdom_1587
GCTAAGAGCACAACAATGGAGGAAACACCTATATGGGAACAATACACAGTGACGCTTCACAGGGCTCCTAGATTTGGGTT
TTGAATTGCAATAGCAGGAGGAAGAAATAATCCTCATTTTCAGAGTGGTGAAACTTCAATAGTGTTGAAAGGAGGTCCAG
CTAAAGGACAACTTCAGGAAAATGATCATGTTGCAATGGTTAATGGTGTTTCCATGGATAATGTGGAACATGCTTTTGCT
GTTCAACAATTAAGGAAAAGTGGGAAAAATGCAAAAATTACCATTCGAAGAAAGAAGAAAGTTCAGATACCTGTAACCCG
TACAGAACCTGAGCCAGTATCTGAAAATGAAGAAGACATTTATGATGAAGAGGTACATGATTCAAAG

Alignment

ORF - retro_mdom_1587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.72 %
• Parental protein coverage: 61.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKSTTMEETAIWEQHTVTLHRAPGFGFGIAISGGRDNPHFQSGETSIVISDVLKGGPAEGQLQENDRVAM
          AKSTTMEET.IWEQ.TVTLHRAP.FGF.IAI.GGR.NPHFQSGETSI....VLKGGPA.GQLQEND.VAM
Retrocopy AKSTTMEETPIWEQYTVTLHRAPRFGF*IAIAGGRNNPHFQSGETSI----VLKGGPAKGQLQENDHVAM

Parental  VNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKKVQIPVTRPEPEPVSENEEDSYDEEVHDSR
          VNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKKVQIPVTR.EPEPVSENEED.YDEEVHDS.
Retrocopy VNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKKVQIPVTRTEPEPVSENEEDIYDEEVHDSK

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	28.37 RPM
SRP007412_cerebellum	0.00 RPM	21.22 RPM
SRP007412_heart	0.00 RPM	39.87 RPM
SRP007412_kidney	0.00 RPM	39.50 RPM
SRP007412_liver	0.00 RPM	12.59 RPM
SRP007412_testis	0.00 RPM	60.11 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1587 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1587 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000028765	1 retrocopy	retro_mdom_1587 ,