RetrogeneDB ID: retro_mdom_902

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:367396890..367397220(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATPIF1
• Ensembl ID: ENSMODG00000010826
• Aliases: None
• Description: ATPase inhibitory factor 1 [Source:HGNC Symbol;Acc:871]

Sequence

>retro_mdom_902
ATATGCTGTACTGTGGCGACAGCAGCTCGACTTGGGCTTGGGCTCTGGGGCTGGAGGACCATGCAGGCCCAGAGCTATAA
CTTGGACTCCAGCCAGTTTAGCACTTTTGGAGGTAAAGGCGGTGGCTCCATCTGAGACACAGGCGGGGCCTTAGGCAGAA
GTGAGAAGGCCGAGGAGGAGCAGTACTTCTTAGAGAAGAACAAAGAGCAACTGGCTGCCCTTAGGAAATACCATCAAGAA
GAAATTAGCCACCACAAGAAGGAGATACAGCATCTGCAGAAAGAAATCAAGAGTCATAAGGGCAAGATTAAACATCTTAA
GCATGATGAT

Alignment

ORF - retro_mdom_902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MACTVATAARLGLGLWGARTMQARSYNLDSRQFSTLGGEGGGSIRDAGGAFSRREKAEEERYFREKNKEQ
          ..CTVATAARLGLGLWG.RTMQA.SYNLDS.QFST.GG.GGGSI.D.GGA..R.EKAEEE.YF.EKNKEQ
Retrocopy ICCTVATAARLGLGLWGWRTMQAQSYNLDSSQFSTFGGKGGGSI*DTGGALGRSEKAEEEQYFLEKNKEQ

Parental  LAALRKYHQEEISHHEKEIQRLQKEIERHKGKIKHLKHDD
          LAALRKYHQEEISHH.KEIQ.LQKEI..HKGKIKHLKHDD
Retrocopy LAALRKYHQEEISHHKKEIQHLQKEIKSHKGKIKHLKHDD

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_902 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_902 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000000170	1 retrocopy	retro_mluc_363,
Monodelphis domestica	ENSMODG00000010826	1 retrocopy	retro_mdom_902 ,
Otolemur garnettii	ENSOGAG00000010337	2 retrocopies	retro_ogar_116, retro_ogar_268,
Rattus norvegicus	ENSRNOG00000013300	1 retrocopy	retro_rnor_2655,