RetrogeneDB ID: retro_mdom_749

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:316619094..316619400(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012167
• Aliases: None
• Description: None

Sequence

>retro_mdom_749
CTCACAGCCTTAAAGGAGAAGTATATGTGATTTGACCTGAACTGTGAAGAAGAAATTGACTTGATGTCCTTGAAGCAGAT
GATGGAGAAGTTGGGTGTCCTGAAGATCCACCTAGAGATGGAGAAGATAATCTCTGAGGTGACAGGTGGGATCAGTGATA
CCATTTCCTATCAGAACATTAAGAATATAATGCTTGGAAAATGTTCAGTAGTCCTCAAGTTAGTCATGATGTTTGAAGGA
AAAGCCAATGAGAGTGCCCCCAACCCTCTCAGCCCTCTTCCTGGAAGAGATATTGCTAGCCTGCCC

Alignment

ORF - retro_mdom_749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.41 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTAFKEKYMEFDLNNEGEIDLMSLKRMMEKLGVPKTHLEMKKIISEVTGGVSDTISYRDFVNMMLGKRSA
          LTA.KEKYM.FDLN.E.EIDLMSLK.MMEKLGV.K.HLEM.KIISEVTGG.SDTISY....N.MLGK.S.
Retrocopy LTALKEKYM*FDLNCEEEIDLMSLKQMMEKLGVLKIHLEMEKIISEVTGGISDTISYQNIKNIMLGKCSV

Parental  VLKLVMMFEGKANESAPKPVGPPPERDIASLP
          VLKLVMMFEGKANESAP.P..P.P.RDIASLP
Retrocopy VLKLVMMFEGKANESAPNPLSPLPGRDIASLP

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	248.41 RPM
SRP007412_cerebellum	0.00 RPM	203.71 RPM
SRP007412_heart	0.00 RPM	14.95 RPM
SRP007412_kidney	0.00 RPM	1976.57 RPM
SRP007412_liver	0.00 RPM	2.52 RPM
SRP007412_testis	0.00 RPM	26.13 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_749 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_749 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
Monodelphis domestica	ENSMODG00000012167	2 retrocopies	retro_mdom_1769, retro_mdom_749 ,
Otolemur garnettii	ENSOGAG00000016759	2 retrocopies	retro_ogar_821, retro_ogar_93,
Tursiops truncatus	ENSTTRG00000003925	1 retrocopy	retro_ttru_959,