RetrogeneDB ID: retro_mdom_180

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:239374556..239375372(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003668
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002880
• Aliases: None
• Description: None

Sequence

>retro_mdom_180
ATGATGATCCAGGGCTTCCAGAGCAGCCGCCAGGACTTCTCCTTCGGGCCCTGGAAGCTGACGGCGGCCAAGACGCACAT
CATGAAGTCGGCCGATGTGGAGAAATTAGCTGATGAGCTCCATATGCCATCTCTTCCTGAAATGATGTTTGGAGACAATG
TTTTAAGAATCCAACATGTTTCTGGCTTTGGAATTGAGTTCAATGCAACAGATGCTTTAAAGTGTGTAAACAACTACCAA
GGAGTGCTTAAGGTGGCATGTGCTGAAGAATGGCAAGAGAGCAGGATGGAGGGTGAGCACTCCAAAGAGATTATTAGACC
ATATGACTGGACCTATACAACAGATTACAAAGGAACATTACTTGGCGAAGCTCTTAAGTTAAAGGTTGTGCCTACAACAG
ATCATATAGACACAGAGAAATTGAAAGCCAGAGAACAGATTAAATTTTTTGAAGAAGTTCTGTTGTTTGAAGATGAACTT
CATGATCATGGAGTTTCAAGCTTAAGTGTGAAAATTAGAGTGATGCCTTCTAGCTTTTTCCTGTTACTGAGATTTTTCTT
AAGAATTGATGGCGTGCTCATCAGGATGAATGACACAAGGCTCTACCATGAGGCTGACAAGACTTACATGTTAAGAGAAT
ACACTTCAAGGGAGAGCAAAATAGCAAATTTAATGCATGTTCCACCAGCCCTCTTTACAGAGCCCAATGAAATATCACAA
TACCTACCTGTAAAGGAGGCAGTATGTGAGAAGCTGGAGTTTCCTGAAAGAATGGATCTTAACCTTGTGGCTACACAGGA
AAATACATGCATGGAA

Alignment

ORF - retro_mdom_180 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMIHGFQSSRQDFSFGPWKLTAAKTHIMKSADVEKLADELHMPSLPEMMFGDNVLRIQHVSGFGIEFNAT
          MMI.GFQSSRQDFSFGPWKLTAAKTHIMKSADVEKLADELHMPSLPEMMFGDNVLRIQHVSGFGIEFNAT
Retrocopy MMIQGFQSSRQDFSFGPWKLTAAKTHIMKSADVEKLADELHMPSLPEMMFGDNVLRIQHVSGFGIEFNAT

Parental  DALKCVNNYQGVLKVACAEEWQESRTEGEHSKEIIRPYDWTYTTDYKGTLLGEALKLKVVPTTDHIDTEK
          DALKCVNNYQGVLKVACAEEWQESR.EGEHSKEIIRPYDWTYTTDYKGTLLGEALKLKVVPTTDHIDTEK
Retrocopy DALKCVNNYQGVLKVACAEEWQESRMEGEHSKEIIRPYDWTYTTDYKGTLLGEALKLKVVPTTDHIDTEK

Parental  LKAREQIKFFEEVLLFEDELHDHGVSSLSVKIRVMPSSFFLLLRFFLRIDGVLIRMNDTRLYHEADKTYM
          LKAREQIKFFEEVLLFEDELHDHGVSSLSVKIRVMPSSFFLLLRFFLRIDGVLIRMNDTRLYHEADKTYM
Retrocopy LKAREQIKFFEEVLLFEDELHDHGVSSLSVKIRVMPSSFFLLLRFFLRIDGVLIRMNDTRLYHEADKTYM

Parental  LREYTSRESKIANLMHVPPALFTEPNEISQYLPVKEAVCEKLEFPERMDLNLVATQENTCME
          LREYTSRESKIANLMHVPPALFTEPNEISQYLPVKEAVCEKLEFPERMDLNLVATQENTCME
Retrocopy LREYTSRESKIANLMHVPPALFTEPNEISQYLPVKEAVCEKLEFPERMDLNLVATQENTCME

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	0.36 RPM	0.00 RPM
SRP007412_cerebellum	0.33 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	0.59 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_180 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_180 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008689	3 retrocopies	retro_chof_1079, retro_chof_1094, retro_chof_1746,
Cavia porcellus	ENSCPOG00000009945	1 retrocopy	retro_cpor_763,
Echinops telfairi	ENSETEG00000005808	1 retrocopy	retro_etel_1273,
Microcebus murinus	ENSMICG00000007808	1 retrocopy	retro_mmur_1335,
Myotis lucifugus	ENSMLUG00000011927	3 retrocopies	retro_mluc_607, retro_mluc_909, retro_mluc_941,
Monodelphis domestica	ENSMODG00000002880	1 retrocopy	retro_mdom_180 ,
Mus musculus	ENSMUSG00000040843	1 retrocopy	retro_mmus_2653,
Ochotona princeps	ENSOPRG00000011313	1 retrocopy	retro_opri_885,
Pteropus vampyrus	ENSPVAG00000005071	1 retrocopy	retro_pvam_257,
Rattus norvegicus	ENSRNOG00000003048	1 retrocopy	retro_rnor_2197,
Sarcophilus harrisii	ENSSHAG00000018932	1 retrocopy	retro_shar_771,
Ictidomys tridecemlineatus	ENSSTOG00000014921	1 retrocopy	retro_itri_1756,
Tupaia belangeri	ENSTBEG00000017081	3 retrocopies	retro_tbel_1717, retro_tbel_2833, retro_tbel_3376,