RetrogeneDB ID: retro_mdom_1442

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:73461456..73461780(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011909
• Aliases: None
• Description: None

Sequence

>retro_mdom_1442
TTTTACCAGAACCTTAAAGACAGAGATGTCCCATTTCCCCAAGCAATGTCGAGAATGAATTTATGAAGTCTTGCAATGAA
GCAAAAGGAAAAGAAAACCATTTATGTTATTACATTGGAGCCAGCAGTGATGCAGCCACTGAGATCAATAAATGAACTGT
CAAAGCCCCTGAGCCACCACATTCCTGTTTAGAAGATCTGTGAAATACTGAAGAAGAAAGACAGTCAAGTATATGAGCTC
AGATATGATAAGCAGATTGACCTGAGCACAACTGATCTGAAGAAACTCAGATTAAAAGAGTTAAAGGATATTCTGGATGA
CTGG

Alignment

ORF - retro_mdom_1442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 60. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FYQDLNDRGVTF-SPSNIENELMKFCNDAKGKENRLCYYIGATSDAATKI-INEVSKPLSHHIPVEKICE
          FYQ.L.DR.V.F.SPSN.ENE.MK.CN.AKGKEN.LCYYIGA.SDAAT.I.INE.SKPLSHHIPV.KICE
Retrocopy FYQNLKDRDVPF<SPSNVENEFMKSCNEAKGKENHLCYYIGASSDAATEI>INELSKPLSHHIPV*KICE

Parental  KLKKKDSQICELKYDKQIDLSTVDLKKLRVKELKKILDDW
          .LKKKDSQ..EL.YDKQIDLST.DLKKLR.KELK.ILDDW
Retrocopy ILKKKDSQVYELRYDKQIDLSTTDLKKLRLKELKDILDDW

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_1442 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1442 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011909	1 retrocopy	retro_mdom_1442 ,