RetrogeneDB ID: retro_mdom_872

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:257938071..257938423(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018053
• Aliases: None
• Description: None

Sequence

>retro_mdom_872
TTTGATTCTTAGACCAAAAATATCTTTGAGAGGAAAGACAATAATAATTCCAGTTTCTACACAGGGGTTTCTATATTCAT
GGCATTTAGTGTTCTTATAATGCTGGTAAGTTCCTTGAATTGCTGTGAGGTCAAGAGTCACAGGACATAATGGGCTTGTT
CTTTGCCTTTTTATTGAGGATTTTTTACTTCAAAATAACTACTGCCATATGAGGTTATTCCCACAAAGATGGGTTGATTT
GTGAGATCCAGACATTTTAGAGGGAAATGTACAAGATCAGAACTAAAGAAGAGGGTATACAAGGACACTCAAAACTATCC
CCTGTGCTTTAGGCTACTGTGGTTTGGCTGGA

Alignment

ORF - retro_mdom_872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.92 %
• Parental protein coverage: 52.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FDTQTKSIFDQEDNNNSSFYTGVYILIGAGALMMLVGFLGCCGAV-QESQCMLGLFFAFLLVIFAIEIAA
          FD..TK.IF...DNNNSSFYTGV.I......L.MLV..L..C..V.QESQ...GLFFAFLL.IF...I..
Retrocopy FDS*TKNIFERKDNNNSSFYTGVSIFMAFSVLIMLVSSLN-CCEV<QESQDIMGLFFAFLLRIFYFKITT

Parental  AIWGYSHKEEVIREVQAFYKETYRKMKDKES-PYKDTLKAIHQALDCCGLTG
          AI.GYSHK...I.E.Q.F..E.Y.K...KE...Y..TLK.I..AL..CGL.G
Retrocopy AI*GYSHKDGLICEIQTF*REMY-KIRTKEE<GYTRTLKTIPCALGYCGLAG

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_872 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_872 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009313	1 retrocopy	retro_eeur_174,
Felis catus	ENSFCAG00000006863	1 retrocopy	retro_fcat_1098,
Myotis lucifugus	ENSMLUG00000006901	1 retrocopy	retro_mluc_2384,
Monodelphis domestica	ENSMODG00000018053	3 retrocopies	retro_mdom_1490, retro_mdom_226, retro_mdom_872 ,
Monodelphis domestica	ENSMODG00000020396	1 retrocopy	retro_mdom_228,
Mus musculus	ENSMUSG00000030342	1 retrocopy	retro_mmus_3022,
Ictidomys tridecemlineatus	ENSSTOG00000001348	1 retrocopy	retro_itri_768,