RetrogeneDB ID: retro_mdom_2004

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:61802164..61802564(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SBDS
• Ensembl ID: ENSMODG00000006644
• Aliases: None
• Description: Shwachman-Bodian-Diamond syndrome [Source:HGNC Symbol;Acc:19440]

Sequence

>retro_mdom_2004
TGTGTTCATCCTGAAACAAAGAAACCATCCACTGTCATCCTCGTTGAAAGAGCAATGAAGGATAGCCACTATTCTGTCAA
GTCCAACAAGCGTACAAAGCAGCAGGCTTTGGAAGTAATAAAACCGTTGAAGGAAAACATGAAGATTGAGGGAGCCCACA
TGAGACTTCCATTCATCCTACCTGAGAGAGAAGGAAAAAAGCTCCAAGAAAAACTGAAACTATTGATCAAGGGCATAGAA
AAGTGAAGACTTTGGTGAACCCTTAGAAACTGTATGTCAAACTGATCTGGGCTGCTTCAGAGAAATTGATGAGCTGAGTC
AGAAAGAGGAGACAAAAGGAAAAGGTTCTTTGGAAGCTCTCAGCTTGAAAGATGTGGAAGAAGGAGATGAGAAATTTGAA

Alignment

ORF - retro_mdom_2004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.34 %
• Parental protein coverage: 52.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVNPETKRPYTVILIERAMKDIHYSVKPNKSTKQQALEVIKQLKESMKIERAHMRLRFILPVREGKKLKE
          CV.PETK.P.TVIL.ERAMKD.HYSVK.NK.TKQQALEVIK.LKE.MKIE.AHMRL.FILP.REGKKL.E
Retrocopy CVHPETKKPSTVILVERAMKDSHYSVKSNKRTKQQALEVIKPLKENMKIEGAHMRLPFILPEREGKKLQE

Parental  KLKPLIKVIE-SEDFGEQLEIVCLIDPGCFREIDELIQR-ETKGKGSLEVLSLKDVEEGDEKFE
          KLK.LIK.IE.SEDFGE.LE.VC..D.GCFREIDEL.Q..ETKGKGSLE.LSLKDVEEGDEKFE
Retrocopy KLKLLIKGIE>SEDFGEPLETVCQTDLGCFREIDELSQKEETKGKGSLEALSLKDVEEGDEKFE

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_2004 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2004 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003795	2 retrocopies	retro_chof_1999, retro_chof_623,
Callithrix jacchus	ENSCJAG00000004283	1 retrocopy	retro_cjac_3984,
Dasypus novemcinctus	ENSDNOG00000016904	1 retrocopy	retro_dnov_748,
Loxodonta africana	ENSLAFG00000008763	1 retrocopy	retro_lafr_920,
Monodelphis domestica	ENSMODG00000006644	1 retrocopy	retro_mdom_2004 ,
Mus musculus	ENSMUSG00000025337	1 retrocopy	retro_mmus_950,
Otolemur garnettii	ENSOGAG00000009011	1 retrocopy	retro_ogar_3368,
Ochotona princeps	ENSOPRG00000008721	6 retrocopies	retro_opri_1179, retro_opri_154, retro_opri_363, retro_opri_484, retro_opri_698, retro_opri_957,
Rattus norvegicus	ENSRNOG00000000888	1 retrocopy	retro_rnor_686,
Ictidomys tridecemlineatus	ENSSTOG00000022203	1 retrocopy	retro_itri_1763,