RetrogeneDB ID: retro_mdom_1063

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:467677757..467678103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB11
• Ensembl ID: ENSMODG00000018491
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa [Source:HGNC Symbol;Acc:20372]

Sequence

>retro_mdom_1063
GTGGTTACCCAGCCCAAAGTGGAAAAGTGGCCCAAGGCACCAGAGGTTGCCTGGCAAGAGGACCCCTAACACAAAGATGT
CAACCTTCATGAGAAGAACCCAGATTCTAATGGTTTTGATGAAGACCCTTTCATAGACCTCTGAACATGAGAATGGCATT
CTTCTTGGGAGTCTCGGTCACCATTGTCCTAGGTTCTACCTTTGTGGCATATCTCCCTGACCACAAGATGAAGGAATGGG
CCTGGAGGGAGGTAGAGATATTGGTGAAGATAAGGGAGAAATAGGTCTTCCTCTTATGGAGTCCAACTATTTTGACTCCA
AGAAGATTATTTTGCCTGATGATGAT

Alignment

ORF - retro_mdom_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.2 %
• Parental protein coverage: 74.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVTPPEVKKRPKAPEVAWQEDPEHEDVNLYEKNPDAHGFDDDPFIDL-WNMRIVFFLGVSVAIVLGSTFV
          VVT.P.V.K.PKAPEVAWQEDP.H.DVNL.EKNPD..GFD.DPFIDL..NMR..FFLGVSV.IVLGSTFV
Retrocopy VVTQPKVEKWPKAPEVAWQEDP*HKDVNLHEKNPDSNGFDEDPFIDL<LNMRMAFFLGVSVTIVLGSTFV

Parental  AYLPDHKMKEWARREAEILVKIRE-TQGLPLMESNYFDPKKIILPDDD
          AYLPDHKMKEWA.RE.EILVKIRE...GLPLMESNYFD.KKIILPDDD
Retrocopy AYLPDHKMKEWAWREVEILVKIRE<EIGLPLMESNYFDSKKIILPDDD

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_1063 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1063 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147123	1 retrocopy	retro_hsap_912,
Macaca mulatta	ENSMMUG00000017422	2 retrocopies	retro_mmul_1116, retro_mmul_830,
Monodelphis domestica	ENSMODG00000018491	1 retrocopy	retro_mdom_1063 ,
Mus musculus	ENSMUSG00000031059	2 retrocopies	retro_mmus_245, retro_mmus_2602,
Pongo abelii	ENSPPYG00000020284	1 retrocopy	retro_pabe_788,
Pan troglodytes	ENSPTRG00000021836	1 retrocopy	retro_ptro_633,
Rattus norvegicus	ENSRNOG00000008329	1 retrocopy	retro_rnor_151,
Ictidomys tridecemlineatus	ENSSTOG00000026821	1 retrocopy	retro_itri_1084,