RetrogeneDB ID: retro_mdom_104

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:33480089..33481055(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003318
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSMODG00000001077
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_mdom_104
TGCTCCTTCGCTCCTACCTTCCTCCCTCCCTCGCTGAGCATGGCCCAGACGCTCGTCCTGGCCTGGCTCCTGGTGGCGGC
AGCGGGCTGGACAGCGGCCCAGAACTGCACCTGCCCCACCAACAAGTGGACCGTCTGCAACCAGGTGGGCGCCAGCTGCC
AGTGCACGGTCCTGGGCTCCAGCCACGTGGTGGACTGCTCCACCTTGACCTCCAAGTGCCTGCTGATGCAGGCGCGCATG
AGGCCGAACAAGCCCCGCAGGCTGATCAATCCCAGCGAGCACGCCGTGGTGGACAACGACGGCCTGTACAACCCGGACTG
CGACAGCGGCGGCCGCTTCAAGGCCCGCCAGTGCAACCAGAGCGACGTGTGCTGGTGCGTCAATTCGGTGGGCGTGCGGC
GCACGGACAAGGGCGACCAGACGCTCAAGTGCGATGAGCTCGTGCGCACCAGCTACATCCTCATCAACCTCCGGCACCAG
GAGCGCGCCCAGGCCTTCAACCACTCGGACCTGAGCCGCGCGCTGCGGCGCCTCTTCCAGGAGCGCTACCAGCTGAGCCC
CAAGTACATCACGGCCGTGGAGTACGAGCAGCCCACTATCCAGATCGAGCTGCAGCAGAACGCCACCCAGAAGGCGCACG
GGGAGGTGGACATCGCCGATGTGGCCTACTACTTTGAGAGGGATATCAAGGGCGAGTCTGTGTTCCACAACCGCCACCTC
AACCTGGAGGTCAGAGGGGAGCCCCTGCGAGTGGAGGACACCATGATCTACTACGTGGACGAGAAGCCCCCCGAGTTCTC
CATGAAGAGGATGACGGCCGGCCTGATTGCCGTCATCGTGGTGGTGGCCCTGGCCATCGTGGCTGGCGTGGTGGTCCTCA
TCATTAGCAACAAGAGAAAGTCAGGAAAGTATGAGAAGGTGGAAATCAAAGAGATGGGCGAAATGAACAAGCGACTCAAC
TTGTAG

Alignment

ORF - retro_mdom_104 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.16 %
• Parental protein coverage: 99.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPPALALGLLLAAA----AVAVSFAQEACYCETNKLTNCTNIPFEGCQCHAIGSSHLITCSKIASKCLIM
          LPP.L.....L..A....A.A...A...C.C.TNK.T.C.......CQC...GSSH...CS...SKCL.M
Retrocopy LPPSLSMAQTLVLAWLLVAAAGWTAAQNCTCPTNKWTVCNQVG-ASCQCTVLGSSHVVDCSTLTSKCLLM

Parental  KAEMLNSKMGRRKKP-EGAIQDNDGIYDPDCDIHGHFKPRQCNGTALCWCVNTAGVRRTDK-ETEIACDE
          .A.M...K..R...P.E.A..DNDG.Y.PDCD..G.FK.RQCN....CWCVN..GVRRTDK......CDE
Retrocopy QARMRPNKPRRLINPSEHAVVDNDGLYNPDCDSGGRFKARQCNQSDVCWCVNSVGVRRTDKGDQTLKCDE

Parental  LVRTYWIIIELKHKTREKPFNTTILENALKEEFQRRYQLNKKYVQNILYENDFITIHLKQNSSQKSTNDV
          LVRT..I.I.L.H..R...FN...L..AL...FQ.RYQL..KY.....YE...I.I.L.QN..QK....V
Retrocopy LVRTSYILINLRHQERAQAFNHSDLSRALRRLFQERYQLSPKYITAVEYEQPTIQIELQQNATQKAHGEV

Parental  DIADVAYYFEKDVKGESLFFSSKINLDINGEKLDLDPAQTLIYYVDEKAPEFSMQGLTAGVIAVIVVVVL
          DIADVAYYFE.D.KGES.F.....NL...GE.L......T.IYYVDEK.PEFSM...TAG.IAVIVVV.L
Retrocopy DIADVAYYFERDIKGESVFHNRHLNLEVRGEPLRVE--DTMIYYVDEKPPEFSMKRMTAGLIAVIVVVAL

Parental  ALVAGIVVLIVSRKKRRTKYEKAEIKEMGEMHRELS
          A.VAG.VVLI.S.K....KYEK.EIKEMGEM...L.
Retrocopy AIVAGVVVLIISNKRKSGKYEKVEIKEMGEMNKRLN

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	5.72 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	72.48 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_104 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_104 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006474	1 retrocopy	retro_btau_66,
Choloepus hoffmanni	ENSCHOG00000013834	1 retrocopy	retro_chof_258,
Callithrix jacchus	ENSCJAG00000000624	1 retrocopy	retro_cjac_3006,
Dasypus novemcinctus	ENSDNOG00000011799	1 retrocopy	retro_dnov_345,
Erinaceus europaeus	ENSEEUG00000009462	1 retrocopy	retro_eeur_151,
Macropus eugenii	ENSMEUG00000015074	2 retrocopies	retro_meug_1984, retro_meug_474,
Microcebus murinus	ENSMICG00000000151	1 retrocopy	retro_mmur_739,
Macaca mulatta	ENSMMUG00000012390	1 retrocopy	retro_mmul_34,
Monodelphis domestica	ENSMODG00000001077	1 retrocopy	retro_mdom_104 ,
Mus musculus	ENSMUSG00000045394	1 retrocopy	retro_mmus_185,
Ochotona princeps	ENSOPRG00000004301	1 retrocopy	retro_opri_1225,
Pelodiscus sinensis	ENSPSIG00000015680	1 retrocopy	retro_psin_22,
Pan troglodytes	ENSPTRG00000011902	1 retrocopy	retro_ptro_92,
Rattus norvegicus	ENSRNOG00000015667	1 retrocopy	retro_rnor_252,
Sus scrofa	ENSSSCG00000008429	1 retrocopy	retro_sscr_69,
Ictidomys tridecemlineatus	ENSSTOG00000008631	1 retrocopy	retro_itri_106,
Tursiops truncatus	ENSTTRG00000004235	2 retrocopies	retro_ttru_21, retro_ttru_394,