RetrogeneDB ID: retro_mdom_1811

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:193777998..193778291(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012580
• Aliases: None
• Description: None

Sequence

>retro_mdom_1811
ATGAAGTTCCTTAGGGCCTCAGAGGAACATCTGAAATAGCATCATGTTGGCCTGAAGGACAGATTGTTTTTCCCCGGGCT
TATGAAATACCTCATTTCAGGGCTTGTTGTGGCCATGGTCTGGGAGGGATTGAATGTGGTGAAGGCAGCAGAGTGATGGT
GGGGGAGACCAACCCAGCTGTTTCCAAGCTAAGCATCATTTCTGGGAACTTCTGCATTCAAGTCAACAGGAACATCATTC
ACCACAGATTCTGTAAAATAGTGCTGAAGAGGAAACCAAGTCTGTGGTCTAAG

Alignment

ORF - retro_mdom_1811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.68 %
• Parental protein coverage: 85.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKFLRASEEHLKQHYVDLKDRPFFPGLVKYMNSGPVVAMVWEGLNVVKT-GRVMLGETNPADSKPGTIRG
          MKFLRASEEHLK.H.V.LKDR.FFPGL.KY..SG.VVAMVWEGLNVVK...RVM.GETNPA.SK...I.G
Retrocopy MKFLRASEEHLK*HHVGLKDRLFFPGLMKYLISGLVVAMVWEGLNVVKA<SRVMVGETNPAVSKLSIISG

Parental  DFCIQVGRNIIHGSDSVKSAEKEISLWFK
          .FCIQV.RNIIH............SLW.K
Retrocopy NFCIQVNRNIIHHRFCKIVLKRKPSLWSK

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_1811 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1811 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 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Monodelphis domestica	ENSMODG00000012580	1 retrocopy	retro_mdom_1811 ,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,