RetrogeneDB ID: retro_mdom_202

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:36594341..36595574(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003697
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EIF4A3
• Ensembl ID: ENSMODG00000002190
• Aliases: None
• Description: eukaryotic translation initiation factor 4A3 [Source:HGNC Symbol;Acc:18683]

Sequence

>retro_mdom_202
ATTGGTGTCCCAGCCACAATGGCTACTTCGGGTTCTGCAGGGAAGAAGCTGCTGAAAGAAGACACAACCAAAGTGGAATT
TGAAACCAGTGAAGAAGTGGACGTGACACCCACTTTTGACTTAGTGGGTTTGCGGGAGGACTTGCTAAGAGGCATCTATG
CCTACGGGTTTGAGAAACCATCTGCTATCCAACAGCGAGCTCTCAAACAAATTATTAAAGGAAGAGACGTCATTGCACAG
TCTCAGTCTGGTACAGGCAAAACAGCAACATTTAGCATTTCAGTCCTCCAATGTTTGGATATTCAGGTGAGAGAAACCCA
GGCTTTGATCTTAGCCCCAACCAGGGAATTAGCTGTACAAATTCAAAAGGTTCTTCTTGCTCTTGGTGACTACATGAATG
TCCAATGTCATGCCTGTATTGGGGGAACAAATGTTGGTGATGATATCAGGCAACTGGATCGTGGACAACATGTTGTTGCT
GGGACACCAGGTCGTGTATTTGATATGATTCGTCGCAGAAGTTTAACAACTCGTGCTATCAAGATGTTGGTTTTGGATGA
AGCTGACCAAATGCTTGACAAAGGATTCAAGGAACAGATTTATGATGTGTACAGATACCTGCCTCCTTCTATTCAAGTGG
TTTTGATCAGTGCCACGTTGCCTCATGAGATCTTAGAAATGACCACTAAATTCATGACTGATCCAATTCGCATCCTGGTA
AGACGTGATGAATTGACTCTCGAGGGAATCAAACAGTTTTTTGTGGCAGTGGAGCGAGAAGAATGGAAATTTGACACTGT
GTGTGACCTTTATGATTCTTTGACCATCACTCAAGCAGTCATCTTTTGTAATACCAAGAGGAAGGTTGACTGGCTGACTG
AGAAAATGAGAGAAGCCAACTTCACTGTTTCATCAATTCATGGAGACATGCCCTCAAGAGAGAGAAAGTTTATCATGAAA
GAGTTCAGATCTGGAGTAAACAGAGTTCTTATTTCTACAGACGTCTGGGCTAGAGGATTAGATGTTCCTCAAGTCTCGCT
CATCATTAACTATGACTTGCCCAATAACAGAGAATTATACATACACAGAATTGGGAGATCAGGTCGATATGGCCGAAAGG
GTGTTGCAATTAACTTTGTGAAGAATGATGATATCCGTATTCTCAGAGATATTGAACAGTACTACTCAACTCAAATTGAT
GAAATGCCCATGAATGTTGCTGATCTCATCTAA

Alignment

ORF - retro_mdom_202 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.37 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIK
          ATMATSGSA.K.LLKE.D.TKVEFETSEEVDVTPTFD..GLREDLLRGIYAYGFEKPSAIQQRA.KQIIK
Retrocopy ATMATSGSAGKKLLKE-DTTKVEFETSEEVDVTPTFDLVGLREDLLRGIYAYGFEKPSAIQQRALKQIIK

Parental  GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGT
          GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQK.LLALGDYMNVQCHACIGGT
Retrocopy GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKVLLALGDYMNVQCHACIGGT

Parental  NVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQV
          NVG.DIR.LD.GQHVVAGTPGRVFDMIRRRSL.TRAIKMLVLDEAD.ML.KGFKEQIYDVYRYLPP..QV
Retrocopy NVGDDIRQLDRGQHVVAGTPGRVFDMIRRRSLTTRAIKMLVLDEADQMLDKGFKEQIYDVYRYLPPSIQV

Parental  VLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFC
          VLISATLPHEILEMT.KFMTDPIRILV.RDELTLEGIKQFFVAVEREEWKFDT.CDLYD.LTITQAVIFC
Retrocopy VLISATLPHEILEMTTKFMTDPIRILVRRDELTLEGIKQFFVAVEREEWKFDTVCDLYDSLTITQAVIFC

Parental  NTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDL
          NTKRKVDWLTEKMREANFTVSS.HGDMP..ER..IMKEFRSG..RVLISTDVWARGLDVPQVSLIINYDL
Retrocopy NTKRKVDWLTEKMREANFTVSSIHGDMPSRERKFIMKEFRSGVNRVLISTDVWARGLDVPQVSLIINYDL

Parental  PNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI
          PNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI
Retrocopy PNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

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_202 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_202 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000009136	2 retrocopies	retro_mmur_444, retro_mmur_50,
Myotis lucifugus	ENSMLUG00000009585	1 retrocopy	retro_mluc_65,
Macaca mulatta	ENSMMUG00000009590	1 retrocopy	retro_mmul_851,
Monodelphis domestica	ENSMODG00000002190	1 retrocopy	retro_mdom_202 ,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Ornithorhynchus anatinus	ENSOANG00000000334	1 retrocopy	retro_oana_47,
Otolemur garnettii	ENSOGAG00000007495	1 retrocopy	retro_ogar_212,