RetrogeneDB ID: retro_mdom_2000

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:51695176..51695955(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5
• Ensembl ID: ENSMODG00000013424
• Aliases: None
• Description: eukaryotic translation initiation factor 5 [Source:HGNC Symbol;Acc:3299]

Sequence

>retro_mdom_2000
GGTTCTGTGTCCAGCAATGAGACAACACCACTACCACCACCACCACCCAATGAACCTAACCCTCCACATGCTGTAGAAGA
TGATGAGGATGAAGATTGGGGAGAGGATACAACTGAAGAAGCTCAAAGGTGTAGAATGGATGAAATTAGTGATCATGCAA
AAGTTCTGACACTTAGTGAAGACCTAGAAAGGGCAGTTGAAGAGTCAATATTTTATTTGACTTTGTGAAGAAAAAGAAAG
AAGAAGGTGTTATTGATACTTCTGACAAAGAAATTGTTGCAGAAGCAGAAAGACTGGACGTAAAAACTATGGGCCCTCTT
GTGTTGGCTGAGGTTCTTTTTAATGAGAAGATTCGAGAACAAATTAAGAAGTATAGACGTCATTTTCTACGATTCTGCCA
CAATAACAAAAAAGCTCAGAGGTACCTTCTTCATGGTTTGGAGTGTGTGGTAGCTATGCATCAAGCTCAGCTCATCTCCA
AAATTCCACATATCTTGAAGGAAATGTATGATGCAGACCTTTTAGAAGAAGAGGTCATCATTAGCTGGTCAGAAAAGGCC
TCTAAGAAATACGTCTCAAAGGAACTTGCCAAATTGATTTGTGTCAAAGCAGAGCCCTTTATAAAATGGCTAAAGGAAGC
AGAAGAGTCTTCTGGTGGAGAAGAGGAAGATGAAGATGAAAATATTGAGGTGGTGTATTCTAAGACTGCCAGCATAACTA
AAGTTGAAACTGTGAAGTCAGCTGATAACAAGGATGATGACATTGACGTTGATGCCATT

Alignment

ORF - retro_mdom_2000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.49 %
• Parental protein coverage: 60.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSVSSNETTP-PPPPPNELNPPHAVEDDEDEDWGEDTTEEAQRRRMDEISDHAKVLTLSDDLERTVEERV
          GSVSSNETTP.PPPPPNE.NPPHAVEDDEDEDWGEDTTEEAQR.RMDEISDHAKVLTLS.DLER.VEE..
Retrocopy GSVSSNETTPLPPPPPNEPNPPHAVEDDEDEDWGEDTTEEAQRCRMDEISDHAKVLTLSEDLERAVEESI

Parental  NILFDFVKKKK-EEGIIDTSDKEIVAEAERLDVKAMGPLVLTEVLFNEKIREQIKKYRRHFLRFCHNNKK
          ..L.....K.K.EEG.IDTSDKEIVAEAERLDVK.MGPLVL.EVLFNEKIREQIKKYRRHFLRFCHNNKK
Retrocopy FYL-TL*RKRK<EEGVIDTSDKEIVAEAERLDVKTMGPLVLAEVLFNEKIREQIKKYRRHFLRFCHNNKK

Parental  AQRYLLHGLECVVAMHQAQLISKIPHILKEMYDADLLEEEVIISWSEKASKKYVSKELAKEIRVKAEPFI
          AQRYLLHGLECVVAMHQAQLISKIPHILKEMYDADLLEEEVIISWSEKASKKYVSKELAK.I.VKAEPFI
Retrocopy AQRYLLHGLECVVAMHQAQLISKIPHILKEMYDADLLEEEVIISWSEKASKKYVSKELAKLICVKAEPFI

Parental  KWLKEAEEESSGGEEEDEDENIEVVYSKTASVPKVETVKSADNKDDDIDIDAI
          KWLKEA.EESSGGEEEDEDENIEVVYSKTAS..KVETVKSADNKDDDID.DAI
Retrocopy KWLKEA-EESSGGEEEDEDENIEVVYSKTASITKVETVKSADNKDDDIDVDAI

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	650.10 RPM
SRP007412_cerebellum	0.00 RPM	848.13 RPM
SRP007412_heart	0.00 RPM	328.73 RPM
SRP007412_kidney	0.00 RPM	701.87 RPM
SRP007412_liver	0.00 RPM	684.24 RPM
SRP007412_testis	0.00 RPM	2503.94 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_2000 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2000 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001236	1 retrocopy	retro_cpor_577,
Erinaceus europaeus	ENSEEUG00000015883	1 retrocopy	retro_eeur_288,
Echinops telfairi	ENSETEG00000015220	2 retrocopies	retro_etel_1843, retro_etel_991,
Homo sapiens	ENSG00000100664	1 retrocopy	retro_hsap_4782,
Monodelphis domestica	ENSMODG00000013424	1 retrocopy	retro_mdom_2000 ,
Nomascus leucogenys	ENSNLEG00000016105	1 retrocopy	retro_nleu_1102,
Pongo abelii	ENSPPYG00000006169	1 retrocopy	retro_pabe_3722,
Pan troglodytes	ENSPTRG00000006753	1 retrocopy	retro_ptro_3183,
Rattus norvegicus	ENSRNOG00000010218	2 retrocopies	retro_rnor_1781, retro_rnor_2459,
Tursiops truncatus	ENSTTRG00000002384	1 retrocopy	retro_ttru_400,