RetrogeneDB ID: retro_mdom_44

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:122293104..122293722(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000029372
• Aliases: None
• Description: None

Sequence

>retro_mdom_44
CAGAAACACTTTCTGATGGAGTTGCCCTGCCTCCCACTGTGCAGAGACAAAGATGTGAAGTTTTGGACCTACTTCAAGAG
GAGAGAGATGCAGGAAATCGTACCTAGATTATTTCTTGGTCCATATTCTTCTGCCTCGAAAAACAAGCTCCCTGAACTGC
AGAAACTTGGAACAACCCATGTCATATGCATAAGGCAAAGCCTTGAAGCAAAGTTTATCCAGCCAAACTTTCCGCAATTC
TTGAAGTATTTAGTCTTGGATGTTGAAGATAATCCAGCTGAAAACATAATGGACTTTTTACCCGCAAGTAAAGAATTTAC
TGATGGAAGTTTGCAAGCAGGAGGAAAAGTACTTGTCCACCGAAACGCAGGATTATCCAGGAGCGCTGCCTTGGTTATTG
CATACAGAATGGAAACGTTTCGAATGACATTCAATGATGCTTTTCTCCACGTGAAAGGAAGAAGGTACTGTATTTGTCCT
AACGATGGATTTATCCACCAGCTTCGGGAATATGAAGCCATCAATCTTGCAAAATTAACTGCGCAGATATCACCACCGGA
ACAGGGAAGATCTTTATCTTTTCTATCTGGTAATAGTGGCAATTTGAAGCGAAGGCAC

Alignment

ORF - retro_mdom_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.35 %
• Parental protein coverage: 90.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEFPTLPQSKE-DAEDWTYPMRREMQEILPGLFLGPYSSAMKSKLPILQKHGITHVICIRQNIEANFIKP
          .E.P.LP.....D...WTY..RREMQEI.P.LFLGPYSSA.K.KLP.LQK.G.THVICIRQ..EA.FI.P
Retrocopy MELPCLPLCRDKDVKFWTYFKRREMQEIVPRLFLGPYSSASKNKLPELQKLGTTHVICIRQSLEAKFIQP

Parental  NFQQLFRYLVLDIADNPVENIIRFFPMTKEFIDGSLQTGGKVLVHGNAGISRSAALVIAYIMETFGVKYR
          NF.Q...YLVLD..DNP.ENI..F.P..KEF.DGSLQ.GGKVLVH.NAG.SRSAALVIAY.METF.....
Retrocopy NFPQFLKYLVLDVEDNPAENIMDFLPASKEFTDGSLQAGGKVLVHRNAGLSRSAALVIAYRMETFRMTFN

Parental  EAFTYVQERRFCINPNAGFVHQLQEYEAIYLAKLTIQMMSPLQLERSLSVQSGTTGSLKRTH
          .AF..V..RR.CI.PN.GF.HQL.EYEAI.LAKLT.Q..SP....RSLS..SG..G.LKR.H
Retrocopy DAFLHVKGRRYCICPNDGFIHQLREYEAINLAKLTAQ-ISPPEQGRSLSFLSGNSGNLKRRH

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	32.42 RPM
SRP007412_cerebellum	0.00 RPM	41.46 RPM
SRP007412_heart	0.00 RPM	49.04 RPM
SRP007412_kidney	0.00 RPM	36.87 RPM
SRP007412_liver	0.00 RPM	74.01 RPM
SRP007412_testis	0.00 RPM	106.66 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_44 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_44 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 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016631	9 retrocopies	retro_dnov_1713, retro_dnov_1720, retro_dnov_1914, retro_dnov_2138, retro_dnov_2186, retro_dnov_2218, retro_dnov_2221, retro_dnov_461, retro_dnov_66,
Echinops telfairi	ENSETEG00000000561	1 retrocopy	retro_etel_1881,
Monodelphis domestica	ENSMODG00000029372	1 retrocopy	retro_mdom_44 ,
Mus musculus	ENSMUSG00000053205	1 retrocopy	retro_mmus_96,
Oryctolagus cuniculus	ENSOCUG00000029442	1 retrocopy	retro_ocun_1555,
Ochotona princeps	ENSOPRG00000016123	1 retrocopy	retro_opri_976,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365,
Vicugna pacos	ENSVPAG00000012229	1 retrocopy	retro_vpac_464,