RetrogeneDB ID: retro_mdom_1918

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:133123505..133124035(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CREG1
• Ensembl ID: ENSMODG00000027768
• Aliases: None
• Description: cellular repressor of E1A-stimulated genes 1 [Source:HGNC Symbol;Acc:2351]

Sequence

>retro_mdom_1918
CCTGTGAAGGTGTACAAAATGCCACCCTGTGAGGACATGGTGCATGCAGTATGGTCAAAGTGCACATCTGCAATTGGGGC
ACACTGGCTACTGAGACTATGTTCACAGCAGTGCGCAGGCGGCCTTTTGCCAACATCTTCTCCCTCAGTGACTGGCCTGT
GGATGTCAGCAGTGGCTTGCCCCATTTTCTACCTAATTCTGCTCCAGCTGTCTGTGGAGGATCTGCAAGTGAATCCAAAT
GCAACTTTGACAATGACTTTGGCATAGACTGATTTTTGCAAGAAGGAGGATTTGATACTCAGTGGCCTCTTTGTGCTCAC
ACAATGCTGTCAGCAAAAGTGACTAAGGTGAATGATACAGAAATGGCCTTTGCAAAAATGTCATTATTCAGTTGCCACCC
TGAAATGGAATCTTGGCCTTTAGATCATAACTGGTTCTTTGCCAAATTGGCTATACCCAACATCTGGGTCATAGACTACT
TTGGTGGAGCCAAAACAGTGACACCTGAAGAATATTATAAAGCCAAACCT

Alignment

ORF - retro_mdom_1918 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.89 %
• Parental protein coverage: 85.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PAKAFELPPREDVARV-ARFIAHVCDWGALATESTLTAVRGRPFANIFSLSDGPVDASTGVPY-FYLSPL
          P.K....PP.ED..........H.C.WG.LATE...TAVR.RPFANIFSLSD.PVD.S.G.P..FYL..L
Retrocopy PVKVYKMPPCEDMVHA<SMVKVHICNWGTLATETMFTAVRRRPFANIFSLSDWPVDVSSGLPH>FYLILL

Parental  QLSVGDLQVNPNASLTLTLAQTDFCKKE-GFDPQSPLCAHIMLSGTITKVNDTETAFAKKSLFSRHPEME
          QLSV.DLQVNPNA.LT.TLA.TDFCKKE.GFD.Q.PLCAH.MLS...TKVNDTE.AFAK.SLFS.HPEME
Retrocopy QLSVEDLQVNPNATLTMTLA*TDFCKKE<GFDTQWPLCAHTMLSAKVTKVNDTEMAFAKMSLFSCHPEME

Parental  SWPSDHNWFFAKLAITNIWVIDYFGGAKTVTPEEYYKAKP
          SWP.DHNWFFAKLAI.NIWVIDYFGGAKTVTPEEYYKAKP
Retrocopy SWPLDHNWFFAKLAIPNIWVIDYFGGAKTVTPEEYYKAKP

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_1918 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1918 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000024	1 retrocopy	retro_amel_792,
Canis familiaris	ENSCAFG00000015414	1 retrocopy	retro_cfam_963,
Monodelphis domestica	ENSMODG00000027768	1 retrocopy	retro_mdom_1918 ,