RetrogeneDB ID: retro_mdom_281

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:121756070..121756466(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024732
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000028393
• Aliases: None
• Description: None

Sequence

>retro_mdom_281
ATGGCGACTTCTCTGTGGAAAGGTTTGGTGGGGCTGGGCCTTTTCGCGCTGGCCCACGCTGCTTTCTCCGCTGCGCAACA
TCGTTCCTATATGCGCTTAACAGAAAAAGAAGATGAAGATCTGCCCATCGATATCGTCCTTCAAACACTGATGGCCTTTG
CTGTTACCTGTTATGGTATAGTCCATCTTGCAGGGGAGTTTAAAGACATGGATGCTACTTCAGAACTGAAAAATAAGACA
CTAGACACATTAAGGAACCACCCATCTTTTTATGTATTTAATCATCGCGGTAGAGTATTGTTCCGGCCTTCAGATATGGT
GTATTCTTCCAACCAAGATGCTTTGTTGTCGAGATCTACAGTGAAGTTACGAAAACTTGAACCTCTGCGTCGTTAA

Alignment

ORF - retro_mdom_281 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.96 %
• Parental protein coverage: 82.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALTWKWLVGLGLIILSHSAFSVAQHRTYMRLTEKKGEALPRDIILQTLLAFVITLYGIVQSVGDFREL
          MA...WK.LVGLGL..L.H.AFS.AQHR.YMRLTEK..E.LP.DI.LQTL.AF..T.YGIV...G.F...
Retrocopy MATSLWKGLVGLGLFALAHAAFSAAQHRSYMRLTEKEDEDLPIDIVLQTLMAFAVTCYGIVHLAGEFKDM

Parental  DATLELENRTMDSLRNHPSFCIFNHRGRVLFRTSKTIVVSS
          DAT.EL.N.T.D.LRNHPSF..FNHRGRVLFR.S.....S.
Retrocopy DATSELKNKTLDTLRNHPSFYVFNHRGRVLFRPSDMVYSSN

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_281 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_281 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025297	2 retrocopies	retro_btau_1566, retro_btau_864,
Cavia porcellus	ENSCPOG00000013476	3 retrocopies	retro_cpor_104, retro_cpor_1171, retro_cpor_979,
Echinops telfairi	ENSETEG00000005810	1 retrocopy	retro_etel_1671,
Monodelphis domestica	ENSMODG00000028393	1 retrocopy	retro_mdom_281 ,
Mus musculus	ENSMUSG00000061273	1 retrocopy	retro_mmus_13,
Oryctolagus cuniculus	ENSOCUG00000029505	1 retrocopy	retro_ocun_660,
Otolemur garnettii	ENSOGAG00000003462	2 retrocopies	retro_ogar_1112, retro_ogar_2224,
Rattus norvegicus	ENSRNOG00000000881	1 retrocopy	retro_rnor_689,
Sus scrofa	ENSSSCG00000025854	1 retrocopy	retro_sscr_908,
Ictidomys tridecemlineatus	ENSSTOG00000004796	1 retrocopy	retro_itri_1421,
Tupaia belangeri	ENSTBEG00000011209	1 retrocopy	retro_tbel_4115,