RetrogeneDB ID: retro_mdom_1926

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:176945432..176945842(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF6
• Ensembl ID: ENSMODG00000019689
• Aliases: None
• Description: eukaryotic translation initiation factor 6 [Source:HGNC Symbol;Acc:6159]

Sequence

>retro_mdom_1926
GTGGGAAATCGACATGGCCTTCCTGTGCCCAACAATACTACAGACCAGGAATTATAGCACACATGAAGCAGTCTCCCGGA
CTCAGTGGGGACCAGATGGAGAAGAGCAACACCTAGCAGCGGGCAATGTTTCCGCCTTTGATGATTAGGTAGCTCTTGTT
CACCCAGACCTAGACAGGGAGACAGAAGAAATTCTAGATGAGGTGCTCAAGGTCGGAAGTCTTCAGACAGACAGTGGCTG
ACCAGGGGCTGGTGGGGAGCTACTGTGCTTTTGGCAATCAGTAAGGGGTGCTGCATCCAAAGACTTCCATTGAAGACCAT
AATGAATTGTCCTCTCTTCTCCAAGCCCCACAGGGGGCTGGCACTGTGAACCTGGGAAGTGAGGTGATAGCAGCTGGAAT
GGTGTTCAAT

Alignment

ORF - retro_mdom_1926 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.82 %
• Parental protein coverage: 55.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VGNRHGLLVPNNTTDQELQHIRNSLPDSVQIR-RVEERLSALGNVTTCNDYVALVHPDLDRETEEILADV
          VGNRHGL.VPNNTTDQEL.H...SLPDSV..R...E..L.A.GNV....D.VALVHPDLDRETEEIL..V
Retrocopy VGNRHGLPVPNNTTDQEL*HT*SSLPDSVGTR>GEEQHLAA-GNVSAFDD*VALVHPDLDRETEEILDEV

Parental  LKV-EVFRQTVADQVLVGSYCVFSNQGGLVHPKTSIEDQDELSSLLQVPLVAGTVNRGSEVIAAGMVVN
          LKV.EVFRQTVADQ.LVGSYC.F.NQ.G..HPKTSIED..ELSSLLQ.P..AGTVN.GSEVIAAGMV.N
Retrocopy LKV>EVFRQTVADQGLVGSYCAFGNQ*GVLHPKTSIEDHNELSSLLQAPQGAGTVNLGSEVIAAGMVFN

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_1926 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1926 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007169	1 retrocopy	retro_meug_26,
Monodelphis domestica	ENSMODG00000019689	1 retrocopy	retro_mdom_1926 ,
Mus musculus	ENSMUSG00000027613	1 retrocopy	retro_mmus_2569,
Oryctolagus cuniculus	ENSOCUG00000010588	1 retrocopy	retro_ocun_1935,
Rattus norvegicus	ENSRNOG00000049497	1 retrocopy	retro_rnor_1067,