RetrogeneDB ID: retro_mdom_1272

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:204508792..204509454(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000010699
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000003574
• Aliases: None
• Description: None

Sequence

>retro_mdom_1272
AGGAAAACATGTCCTCCAGACCTGAAGGACATCCTGCAGATCTTTCAGAAGATTTGGAGAATCCTGACTGGAAGATGAGA
GAGTCTGAAGAACCTAGTTCAGTCAGTTCAAGTTCAAGCTCCAACTCCAGCTTTACTCCATCCCAGTCCAGACAACAAGG
TCCATTAAGGTCTATAATGGAAGATCTGCATTCTGATGACAATGAAGATGAATCAGAGGAGGCAGATGAGAATGACAATG
ACTTGGAGATGGAGAGACCAATAAATAGCGGAGGAGGGAGTCGAAGTCTCAGTTAACTTAAGTGATGGCGGCAACAGCGA
AAGTAGTTCTGCTCCTTCCCCTCTAAGGCACGAACCACTACCGACTTTATTAAAAACTTACAGCAACCAGATTTAGAAGT
GAAAAGTCCAGTAAAGCAAAGCAAATCTGATAAGCAAATTAAGAATGGGGATTGTGACAAGGCATATCTAGATGAACTAG
AAGAACTCCATAGAAGGTTAATGACATTACTGGAACGACATGTACTTCAACAGATTGTAAACCTTATAGAAGAAACTGGA
CACTTTCATATCATGAACACAACCTCTGACTTTGACCTTTGCTCTCTGTATAAAACCACAGTCCGTAAACTACAGAGTTA
CCTGGAAACATCTGGAACATCC

Alignment

ORF - retro_mdom_1272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 69.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKSTLPPFDDIVD-PNDSDMEENMSSKSESEQPSPASSSSSSSSSFTPSQSRQQGPLRSIMKDLHSDDNE
          .K...P...DI.......D.E.......ESE.PS..SSSSSS.SSFTPSQSRQQGPLRSIM.DLHSDDNE
Retrocopy RKTCPPDLKDILQ<DLSEDLENPDWKMRESEEPSSVSSSSSSNSSFTPSQSRQQGPLRSIMEDLHSDDNE

Parental  DESEEADENDNDSEMERPINTRGGSRSR-RVSLSDGSDSESSSASSPLRHEPPPPLLKTNSNQI-LEVKS
          DESEEADENDND.EMERPIN..GG......V.LSDG..SESSSA.SPLRHEP.P.LLKT.SNQI.LEVKS
Retrocopy DESEEADENDNDLEMERPINS-GGGSRS>SVNLSDGGNSESSSAPSPLRHEPLPTLLKTYSNQI<LEVKS

Parental  PIKQSKSDKQIKNGDCDKAYLDELVELHRRLMTLRERHVLQQIVNLIEETGHFHITNTTFDFDLCSLDKT
          P.KQSKSDKQIKNGDCDKAYLDEL.ELHRRLMTL.ERHVLQQIVNLIEETGHFHI.NTT.DFDLCSL.KT
Retrocopy PVKQSKSDKQIKNGDCDKAYLDELEELHRRLMTLLERHVLQQIVNLIEETGHFHIMNTTSDFDLCSLYKT

Parental  TVRKLQSYLETSGTS
          TVRKLQSYLETSGTS
Retrocopy TVRKLQSYLETSGTS

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_1272 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1272 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000003574	1 retrocopy	retro_mdom_1272 ,
Mustela putorius furo	ENSMPUG00000015992	1 retrocopy	retro_mputfur_630,