RetrogeneDB ID: retro_mdom_1713

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:47048932..47049375(+)
• Located in intron of: ENSMODG00000000049

Retrocopy information

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

Parental gene information

• Parental gene symbol: EDF1
• Ensembl ID: ENSMODG00000017329
• Aliases: None
• Description: endothelial differentiation-related factor 1 [Source:HGNC Symbol;Acc:3164]

Sequence

>retro_mdom_1713
ATGGCCGAGAGTGACTGGGACATGGTGATGGCTCTGCACAAGGAGTGCTCCACAGCAGCCCAGGACAAGTTCAAGCTGGC
CATATTAGCAGCTCAGAGAAAGGGAGATGTGGAGACTTCCAAAAAATGGGTTGCTGACCAAAACAAACAGCACTCTATCA
CAAAGAACACAGCCAAGCTGGATTGAGAGACTGAAGAATTTCACCATGACAGAGTCATTCTAGAAGTTGGCTAAGTGATC
CTAGAGGGCTGGCAGAGCAACGGACTGAAACAGAAGGATCTGGCAAAAAAAAATCAATGAAAAGCCCCAAGTTGTTGCTG
ACTCTTAGTGCAGACAGGCCATTCCTTAATAACCAGGTGTTGGGCAAGATTGAAAGAGCCAGTGGTCTCAAGCTTCGTGG
AAAGGACATTGGAAAGCCTCTTGAGACAGGACCAAAGGGGAAA

Alignment

ORF - retro_mdom_1713 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAESDWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNKQHSITKNTAKLDRETEELHH
          MAESDWD.V..L.K...TAAQ.K.K.AILAAQR.G.DVETSKKW.A.QNKQHSITKNTAKLD.ETEE.HH
Retrocopy MAESDWDMVMALHKECSTAAQDKFKLAILAAQRKG-DVETSKKWVADQNKQHSITKNTAKLD*ETEEFHH

Parental  DRVTLEVGKVIQQGRQSKGLTQKDL-ATKINEKPQVIADYECGRAIP-NNQVLGKIERAIGLKLRGKDIG
          DRV.LEVG.VI..G.QS.GL.QKDL.....NEKPQV.AD..C..AIP.NNQVLGKIERA.GLKLRGKDIG
Retrocopy DRVILEVG*VILEGWQSNGLKQKDL>XXXXNEKPQVVADS*CRQAIP>NNQVLGKIERASGLKLRGKDIG

Parental  KPLETGPKGK
          KPLETGPKGK
Retrocopy KPLETGPKGK

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	385.24 RPM
SRP007412_cerebellum	0.00 RPM	375.42 RPM
SRP007412_heart	0.00 RPM	386.94 RPM
SRP007412_kidney	0.00 RPM	513.56 RPM
SRP007412_liver	0.00 RPM	339.35 RPM
SRP007412_testis	0.00 RPM	997.69 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1713 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1713 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 15 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013266	2 retrocopies	retro_amel_1569, retro_amel_996,
Canis familiaris	ENSCAFG00000019544	4 retrocopies	retro_cfam_1283, retro_cfam_1812, retro_cfam_363, retro_cfam_895,
Callithrix jacchus	ENSCJAG00000011166	1 retrocopy	retro_cjac_374,
Erinaceus europaeus	ENSEEUG00000009565	1 retrocopy	retro_eeur_635,
Loxodonta africana	ENSLAFG00000026812	1 retrocopy	retro_lafr_751,
Macropus eugenii	ENSMEUG00000015037	7 retrocopies	retro_meug_108, retro_meug_1742, retro_meug_1805, retro_meug_2070, retro_meug_38, retro_meug_598, retro_meug_773,
Microcebus murinus	ENSMICG00000016498	1 retrocopy	retro_mmur_312,
Macaca mulatta	ENSMMUG00000005051	1 retrocopy	retro_mmul_89,
Monodelphis domestica	ENSMODG00000017329	1 retrocopy	retro_mdom_1713 ,
Mustela putorius furo	ENSMPUG00000011008	1 retrocopy	retro_mputfur_1377,
Mus musculus	ENSMUSG00000015092	3 retrocopies	retro_mmus_3324, retro_mmus_688, retro_mmus_809,
Rattus norvegicus	ENSRNOG00000016272	4 retrocopies	retro_rnor_1407, retro_rnor_2005, retro_rnor_2007, retro_rnor_2616,
Sorex araneus	ENSSARG00000007191	1 retrocopy	retro_sara_39,
Tupaia belangeri	ENSTBEG00000014060	4 retrocopies	retro_tbel_1404, retro_tbel_1950, retro_tbel_3538, retro_tbel_967,
Tursiops truncatus	ENSTTRG00000002668	2 retrocopies	retro_ttru_165, retro_ttru_894,