RetrogeneDB ID: retro_mdom_973

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:86278421..86279334(+)
• Located in intron of: ENSMODG00000000317

Retrocopy information

• Ensembl ID: ENSMODG00000000321
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000023336
• Aliases: None
• Description: None

Sequence

>retro_mdom_973
CTTCATGAGTGTATCTCCATCCACGTGGGACAGGCGGGGGTCCAAATTGGCAATGCCTGCTGGGAATTGTATTGTCTGAA
GCATGGAATTCAACCAGATGGTCAGATGCCAAGTGATAAAACTATAGGGGAGGAGACGATTCCTTTAACATGTTCTTTAG
TGAGACGGGGGCTGGCAAGCATGTGCCCAGAGCTGTGTTTGTGGATCTGGAGCCGACTGTGGTGGATGAAGTCTGGTCAG
GCACATACAGGCTTCTTTTCCATCCCGAGCAGCTGATAACTGGAAAGGAGGATGCAGCCAATAATTATGCCAGAGGCCAT
TACACCATCAGCAAGCAGATTGTTGATCTGGTCCTTGACAGGATTTGCAACCTGGCGGATCTGTGTACTGGCCCGCAGGG
CTTCCTCATCTTCCATAGCTTTGGCGGAGGCAAGGGCTCTGGATTTGCCTCTCTGCTCATGGAGAGGCTCTCCATGGATT
ATGGCAAGAAGTCCAAGCTCGAATTCACCATTTACCCAGCACCCCCGGTCTCCACGGTGGTCGTGGAGCCCTACAACTCC
ATCCTCACCACTCACACGACCCTGGAATACTCCGACTATGCCTTCATGGTTGACAATGAAGCCATATACAACATATGTCG
GTGCAACCTGGACATCGAGAAGCCAACCTACACCAACCTGAATCGGCTCATCAGGCAGATCGTCTCTTCCATAAGGGCCT
CACTGCGCTTTGACGGGGCCCTGAACCTCGACCTGACAGAGTTTCAGACCAACCTGGTGCCCTACCCGCCCATCTACTTT
CCCTGGCCACCTACACCCCCGTCATCTCTGGCAAGAAAGCCTACCAGGAGCAGCTGTCAGTGGCGGAGATCACCAATGCC
TGCTTTGAGCCCCCCAACCAGACAATGACCTGC

Alignment

ORF - retro_mdom_973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.95 %
• Parental protein coverage: 67.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIG-GGDDSFNTFFSETGAGKHVPRAVFVD
          ..ECISIHVGQAGVQIGNACWELYCL.HGIQPDGQMPSDKTIG.GGDDSFN.FFSETGAGKHVPRAVFVD
Retrocopy LHECISIHVGQAGVQIGNACWELYCLKHGIQPDGQMPSDKTIG<GGDDSFNMFFSETGAGKHVPRAVFVD

Parental  LEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDLVLDRIRKLADLCTGLQGFLIFH
          LEPTVVDEV..GTYR.LFHPEQLITGKEDAANNYARGHYTI.K.IVDLVLDRI..LADLCTG.QGFLIFH
Retrocopy LEPTVVDEVWSGTYRLLFHPEQLITGKEDAANNYARGHYTISKQIVDLVLDRICNLADLCTGPQGFLIFH

Parental  SFGGGTGSGFASLLMERLSVDYGKKSKLEFAIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAI
          SFGGG.GSGFASLLMERLS.DYGKKSKLEF.IYPAP.VST.VVEPYNSILTTHTTLE.SD.AFMVDNEAI
Retrocopy SFGGGKGSGFASLLMERLSMDYGKKSKLEFTIYPAPPVSTVVVEPYNSILTTHTTLEYSDYAFMVDNEAI

Parental  YDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFP-LATYAPVISA
          Y.ICR.NLDIE.PTYTNLNRLI.QIVSSI.ASLRFDGALN.DLTEFQTNLVPYP.I.FP.LATY.PVIS.
Retrocopy YNICRCNLDIEKPTYTNLNRLIRQIVSSIRASLRFDGALNLDLTEFQTNLVPYPPIYFP<LATYTPVISG

Parental  EKAYHEQLSVAEITNACFEPANQMVKC
          .KAY.EQLSVAEITNACFEP.NQ...C
Retrocopy KKAYQEQLSVAEITNACFEPPNQTMTC

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_973 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_973 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000014403	1 retrocopy	retro_ecab_318,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348,
Monodelphis domestica	ENSMODG00000023336	1 retrocopy	retro_mdom_973 ,
Mustela putorius furo	ENSMPUG00000003660	1 retrocopy	retro_mputfur_130,
Mus musculus	ENSMUSG00000067338	1 retrocopy	retro_mmus_3356,