RetrogeneDB ID: retro_meug_474

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold11990:20095..20713(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMEUG00000012302
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSMEUG00000015074
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_meug_474
GTGGCGGCCGCTGGCTGGACAGCGGCTCAGAACTGCACCTGCCCCACCAACAAGTGGACGATCTGCAACCCGGCGGGCTC
TGGGGGCAGCTGTCAGTGCACCGTGCTGGGCTCCAACCACGTGGTGGACTGCACCACCCTGACCTCTAAGTGCCTGCTCA
TGAAGGCGCGCATGAACCCGCACAAACCCCGCAGTGTGATCAAACCCAGTGAGCACGCCATAGTGGACAACGACGGTCTC
TACAACCCGGACTGTGACAGCTGGGGCCACTTCAAGGCGCGCCAGTGCAACCAGAGCGACGTGTGCTGGTGCGTTAACTC
GGTGGGCGTGCGGCGGACCGATAAGGGGGACCAGACGCTCAAGTGTGAAGAGCTGGTGCGCACCAGCTACATCCTCATCC
ACCTACGGCACCAGGAGCGCTCCAAAGCCTTCAACCACTCGGAGCTCAGCCAGACCTTGCGGCGCCTCTTCCACGAGCGC
TACCAGCTGAGCCCCAAGTACATCACGGCCGTAGAGTACGAGCGCCCCACCATCCAGATCGAGCTGCAGCAAAACGCCTC
CCAGAAGGCCCACGGCGACGTGGACATCGCCGATGTGGCCTATTACTTCGAGAGGGAC

Alignment

ORF - retro_meug_474 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.97 %
• Parental protein coverage: 63.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTPAREPVAGACFCETNKLTNCTEI-SPDVCQCQAIGSPNIVTCSQLATKCLVMKAEMTNSKSGRRKKP-
          V..A....A..C.C.TNK.T.C....S...CQC...GS...V.C..L..KCL.MKA.M...K.....KP.
Retrocopy VAAAGWTAAQNCTCPTNKWTICNPAGSGGSCQCTVLGSNHVVDCTTLTSKCLLMKARMNPHKPRSVIKPS

Parental  EGAITDNDGIYDPDCDARGLFKPRQCNGTALCWCVNTAGVRRTDK-DSEISCSELVRTYWIIIELRHKTR
          E.AI.DNDG.Y.PDCD..G.FK.RQCN....CWCVN..GVRRTDK.D....C.ELVRT..I.I.LRH..R
Retrocopy EHAIVDNDGLYNPDCDSWGHFKARQCNQSDVCWCVNSVGVRRTDKGDQTLKCEELVRTSYILIHLRHQER

Parental  EKPFDNTAL-ENHQTGISARYQLNPKYIKQILYEDDVITIDLVQNSTQKSSNEVDIADVAYYFEKD
          .K.F....L..........RYQL.PKYI....YE...I.I.L.QN..QK....VDIADVAYYFE.D
Retrocopy SKAFNHSELSQTLRRLFHERYQLSPKYITAVEYERPTIQIELQQNASQKAHGDVDIADVAYYFERD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_474 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_474 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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,