RetrogeneDB ID: retro_mdom_608

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:515473403..515473862(-)
• Located in intron of: ENSMODG00000015479

Retrocopy information

• Ensembl ID: ENSMODG00000023209
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SAP30
• Ensembl ID: ENSMODG00000003536
• Aliases: None
• Description: Sin3A-associated protein, 30kDa [Source:HGNC Symbol;Acc:10532]

Sequence

>retro_mdom_608
GGCCAGAGCTGCTGCCTGATCGAGGACGGGGAGCGTTGTGTCCGGCCTGCCGGCAACAGCTCCTTCAGCAAGAGGATCCA
AAAGAGCATCTCACAGAAGAAACTCCGACTGGACATCGACAAGAGCGTAAGACATCTGTATATCTGTGATTTTCACAAAA
ATTTCATCCAGAGTGTACGAAATAAAAGGAAGAGAAAGACCAGTGATGATGGCGGAGATTCTCCTGAGCACGAAACAGAC
ATCCCTGAGGTTGATTTGTACCAGCTGCAGGTGAATACATTGAGGTGCTACAAAAGGCATTACAAGTTACAGACCAGACC
AGGATTCAACAAGGCACAGCTAGCAGAAACTGTCAGTTGTCACTTCCAGAACATCCCAGTGAACGAGAAAGAGACCCTTG
CTTATTCCATCTATATGGTGAAGAGTAACAAGAGTAGACTGGACCAGAAAGCAGAGAGT

Alignment

ORF - retro_mdom_608 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.38 %
• Parental protein coverage: 67.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQLCCLREDGERCSRAAGNASFSKRIQKSISQKKVKIDLDKTARHLYICDFHKNLIQSVRNRRKRKGSDD
          GQ.CCL.EDGERC.R.AGN.SFSKRIQKSISQKK...D.DK..RHLYICDFHKN.IQSVRN.RKRK.SDD
Retrocopy GQSCCLIEDGERCVRPAGNSSFSKRIQKSISQKKLRLDIDKSVRHLYICDFHKNFIQSVRNKRKRKTSDD

Parental  DGGDSPVQDIDTPEVDLYQLQVNTLRRYKRHFKLPTRPGLNKAQLVEIVGCHFRSIPVNEKDTLTYFIYS
          .GGDSP....D.PEVDLYQLQVNTLR.YKRH.KL.TRPG.NKAQL.E.V.CHF..IPVNEK.TL.Y.IY.
Retrocopy -GGDSPEHETDIPEVDLYQLQVNTLRCYKRHYKLQTRPGFNKAQLAETVSCHFQNIPVNEKETLAYSIYM

Parental  VKNDKNKPDLKIDS
          VK..K...D.K..S
Retrocopy VKSNKSRLDQKAES

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	31.11 RPM	0.00 RPM
SRP007412_cerebellum	15.02 RPM	0.00 RPM
SRP007412_heart	20.93 RPM	0.00 RPM
SRP007412_kidney	25.02 RPM	0.00 RPM
SRP007412_liver	6.04 RPM	0.00 RPM
SRP007412_testis	12.96 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_608 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_608 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164105	1 retrocopy	retro_hsap_2864,
Gorilla gorilla	ENSGGOG00000005082	2 retrocopies	retro_ggor_1980, retro_ggor_3072,
Macaca mulatta	ENSMMUG00000002401	1 retrocopy	retro_mmul_1467,
Monodelphis domestica	ENSMODG00000003536	1 retrocopy	retro_mdom_608 ,
Nomascus leucogenys	ENSNLEG00000006666	1 retrocopy	retro_nleu_605,
Pongo abelii	ENSPPYG00000015205	1 retrocopy	retro_pabe_2366,
Pan troglodytes	ENSPTRG00000016598	1 retrocopy	retro_ptro_1936,