RetrogeneDB ID: retro_mdom_307

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:69016373..69016819(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BIRC5
• Ensembl ID: ENSMODG00000001871
• Aliases: None
• Description: baculoviral IAP repeat containing 5 [Source:HGNC Symbol;Acc:593]

Sequence

>retro_mdom_307
ATGTTCTGCATTAGAGTTGTCAAGAAGAGCATCCTCCTGCTACCTCCAATGTGGCAACTCTACCTGCTAGACACCCACAT
CTCTACATTCCAGAACTGGTCCTTTATGGAAGACTGAGCCTGCGCACAGGAGCAGATGGCTAAAGCTGGGTTCGTCCATT
GCCCAAGTGAGAATGAGCCTGATTTAGCCCAGTGCTTCTTCTATTTCAAGGAACTATAGGAATGGGAACAAAAAGATGAA
CCTATGTTGGATCGTAAAAAGAACTTGTCTAGTTGTGCCTTCATCTTCATTAAGAAGATTGAAGATTTAACACTCAATGA
ATTCCTGAAACTGGACAAAGAAAGAGCCAAAAACAAGACTGAAAAGGAATCCTCTCAGAAAGAATTGAATTTGAAGAGCA
TACAAAGGAAGTAAGGCATGACATTGAGCAATTGGCTGCTTTGGAG

Alignment

ORF - retro_mdom_307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVCVSGTKMSVPPLPPMWQLYLLDTRISTFQNWPFTEDCACTPERMAEAGFIHCPSENEPDLAQCFFCFK
          M.C....K.S...LPPMWQLYLLDT.ISTFQNW.F.ED.AC..E.MA.AGF.HCPSENEPDLAQCFF.FK
Retrocopy MFCIRVVKKSILLLPPMWQLYLLDTHISTFQNWSFMED*ACAQEQMAKAGFVHCPSENEPDLAQCFFYFK

Parental  ELEGWEPEDDPMLEHKKHSSSCAFISIKKKIEDLTLNEFLKLDKERAKNKIEKETSRK-RTEFEEHAKEV
          EL..WE..D.PML..KK..SSCAFI.I.KKIEDLTLNEFLKLDKERAKNK.EKE.S.K.R.EFEEH.KEV
Retrocopy EL*EWEQKDEPMLDRKKNLSSCAFIFI-KKIEDLTLNEFLKLDKERAKNKTEKESSQK<RIEFEEHTKEV

Parental  RHDIEQLAALE
          RHDIEQLAALE
Retrocopy RHDIEQLAALE

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	0.39 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_307 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_307 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013573	1 retrocopy	retro_btau_1347,
Cavia porcellus	ENSCPOG00000027390	1 retrocopy	retro_cpor_1355,
Equus caballus	ENSECAG00000008466	1 retrocopy	retro_ecab_100,
Myotis lucifugus	ENSMLUG00000006281	1 retrocopy	retro_mluc_254,
Macaca mulatta	ENSMMUG00000013767	1 retrocopy	retro_mmul_19,
Monodelphis domestica	ENSMODG00000001871	2 retrocopies	retro_mdom_307 , retro_mdom_996,