RetrogeneDB ID: retro_mdom_1389

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:258461991..258462378(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011375
• Aliases: None
• Description: None

Sequence

>retro_mdom_1389
AGACAAAGGAAGCAGCATGAAGAAATGAAATTGGTCCTCACAATGGCCTATCCAATCACCAAAATACAAATAGAATTCAA
AAACCAGAGCAGGAAAAAAAAATCTCTAGTAGCTCATTTTCTGCCACATATGCCTCATGTAAGTGAACGCCTGATGAAAA
GAAGTTTAAAGTCTGATGACCTGAGATATTTGACATCTGGGTAGCTACAAGTGCTAGTCAATGACCCCCCACTCCTGGGT
AGAGAGCATGAATGAAGAGACAGTTCAGCTGTTTCTCATTTGAGATGGATTGAATGCAGAACAAGATAATGTCGTTTAAC
ACAGAAGATTTTAACTGGCCTTGCTATAAGTTAGCAGAAATTCATGGCTAAGAAAATGCATATGAAA

Alignment

ORF - retro_mdom_1389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.2 %
• Parental protein coverage: 51.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RQRKLQAEAKMALAMAKPMAKMQVEVEKQNRKK-SPVADLLPHMPHISECLMKRSLKPTDLRDMTIGQLQ
          RQRK...E.K..L.MA.P..K.Q.E...Q.R...S.VA..LPHMPH.SE.LMKRSLK..DLR..T.G.LQ
Retrocopy RQRKQHEEMKLVLTMAYPITKIQIEFKNQSRXXXSLVAHFLPHMPHVSERLMKRSLKSDDLRYLTSG*LQ

Parental  VIVND-LHSQIESLNEELVQLLLIRDELHTEQDAML-VDIEDLTRHAESQQKHLAEKMPAK
          V.VND..HS..ES.NEE.VQL.LI.D.L..EQD.........LT..A.S.QK..A.KM..K
Retrocopy VLVND>PHSWVESMNEETVQLFLI*DGLNAEQDNVV<LTQKILTGLAIS*QKFMAKKMHMK

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_1389 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1389 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	ENSMODG00000011375	1 retrocopy	retro_mdom_1389 ,
Ictidomys tridecemlineatus	ENSSTOG00000014607	1 retrocopy	retro_itri_277,