RetrogeneDB ID: retro_mdom_712

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:181914285..181915294(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000014887
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000006756
• Aliases: None
• Description: None

Sequence

>retro_mdom_712
AAGATGATTTCCTTCACGCCTCTCTCGGTGCCATGGAAGAGGTGGCTGCAGACTCTAGCTGCTCTTCAGTGGGTTTTCAG
TTTCCTGGGTTTGGGCATAGTCTGCATAGTCATCTTCATTGGCCTTTTCTTCACCCACTTTTGGTTCCTCAGCATGCTAT
CTATACTCAGCCTGGTGGTACCTGGACAGAGATACCCCAAGAAAAGTTGGGAGACAGATCCAGACCATAAAGAGATGGTA
TATGTGGAAGTACCTGGCAGACTACTTTCCTGTCTCACTCATCAAGACAGTGGATTTGGACCCAAAACAGAACTATATTG
CTGGCTTCCACCCTCATGGTGTCCTGGCTACTGGAGCTTTCTCCAACTTCTGTACTGAAGCCACTGGTTTTTCTTCTGTA
TTTCCTGGGATCCACCCCCACCTGATGATGCTGACTTTGTGGTTCCGAAATCCCTTTTTCAGGGATTATATCATGAGTGG
AGGTTTAGTCACTTTGGAGAAGGAGTGTGTCTCATATTTGCTGAGCAAGAAGGGAGGTGTAAACTTGCTGGTGATTATCG
TGGGAGGGGCCCAGGAGGCCCTGGATGTCCGGCCTGGAAGCTACACACTACTGCTGAGGAACCAGAAAGGATTTGTTAAA
CTCGCCTTGCTTCATGGGGCATCTCTGCTGCCTATATTCTCCTTTGGGGAAAATGAACTCTTTGACCAAATGGACAATCC
TTCAGGATCCTGGCTTCAATGGATCCAGGAAAAACTGCAGAAGGTCATGGGCATCTCCCTCCCAGTCTTCCATGGCCAGG
GGATCTTCCAGTACAGTTTTGGCCTGTTCCCTTACCGGAGGCAAATCACTACTGTAGTGGGGAAGCCCATCAAGGTGAAG
CAAAATATCAACCCAAGCTCAGATGAAGTGGACCATCTGCATCAGCAGTACATGACAGAACTGTGTAACCTCTTTGAAAC
CCACAAGATAAAATACAACGTCCCCCCAGAGCAGCACCTGGAGTTCCGA

Alignment

ORF - retro_mdom_712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMISFAPLSVPLKRRLQTLAALQWVFSFLGLGIVCVVIFIGLFFTRFWFLSML-YSAWWY-LDRDTPRKG
          KMISF.PLSVP.KR.LQTLAALQWVFSFLGLGIVC.VIFIGLFFT.FWFLSML.....W..LDRDTPRK.
Retrocopy KMISFTPLSVPWKRWLQTLAALQWVFSFLGLGIVCIVIFIGLFFTHFWFLSML>LYSAWWYLDRDTPRKV

Parental  GRQIQTIKRWCVWKYLADYFPVSLIKTVDLDPTQNYIAGFHPHGVLATGAFTNFCTEATGFSSVFPGIRP
          GRQIQTIKRW..WKYLADYFPVSLIKTVDLDP.QNYIAGFHPHGVLATGAF.NFCTEATGFSSVFPGI.P
Retrocopy GRQIQTIKRWYMWKYLADYFPVSLIKTVDLDPKQNYIAGFHPHGVLATGAFSNFCTEATGFSSVFPGIHP

Parental  HLMMLTLWFRIPFFRDYIMSGGMFTSEKECVSYLLSKKGGGNLMVIIVGGAQEALDARPGSYTLLLRNRK
          HLMMLTLWFR.PFFRDYIMSGG..T.EKECVSYLLSKKGG.NL.VIIVGGAQEALD.RPGSYTLLLRN.K
Retrocopy HLMMLTLWFRNPFFRDYIMSGGLVTLEKECVSYLLSKKGGVNLLVIIVGGAQEALDVRPGSYTLLLRNQK

Parental  GFVKLALLHGASLLPIFSFGENELFDQMDNPSGSWLRWIQEKLQKVMGISLPVFHGRGIFQYSFGLLPYR
          GFVKLALLHGASLLPIFSFGENELFDQMDNPSGSWL.WIQEKLQKVMGISLPVFHG.GIFQYSFGL.PYR
Retrocopy GFVKLALLHGASLLPIFSFGENELFDQMDNPSGSWLQWIQEKLQKVMGISLPVFHGQGIFQYSFGLFPYR

Parental  RQITTVVGKPIKVKQNINPSSDEVDRLHQQYMTELCNLFETHKIKYNVPPEQHLEFR
          RQITTVVGKPIKVKQNINPSSDEVD.LHQQYMTELCNLFETHKIKYNVPPEQHLEFR
Retrocopy RQITTVVGKPIKVKQNINPSSDEVDHLHQQYMTELCNLFETHKIKYNVPPEQHLEFR

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_712 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_712 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001166	1 retrocopy	retro_meug_442,
Monodelphis domestica	ENSMODG00000006756	3 retrocopies	retro_mdom_126, retro_mdom_1269, retro_mdom_712 ,
Sarcophilus harrisii	ENSSHAG00000001147	1 retrocopy	retro_shar_583,