RetrogeneDB ID: retro_ttru_394

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2118:133339..133813(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSTTRG00000004235
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_ttru_394
AGAGAAAAACCTTATGAGGATCAAAGTTTGTACACTGCACTCAAGGAGGTAATCATAAGTCGTTATCAACTGGATCCAAA
ATATATCACAGATGTTCTGTATGAGAATGATGTTCTCACTGTTGATCTGGTACAAAATTCTCAGAAAATTCAGAATGATG
TGGACATAGATGATGTGGCTTATTATTTTGAAAAAGATGTTAATGGTGAATCCTTGTTCCAGTCCAAAAGGATGGGCCTG
AAAGTAAATGGGGAACTACTGGATCTGGATCCTGGTTGAACTTCAATTTACTATGTTGATGAAAAACCACCTGAATTGTC
AGTGCAGGGTCTACAAGCTGGAATTATCTCTGTCGTTGTGGTTGTGGCGATAGCAGCTACTGCTGGAATCATGCTGGTGG
TTTCCAGAAAGAAAAGAACGGCAAAGTATGAGAAAGCTGAGATGAAGGACATGGGTGAGGTGCATTGGGAACTT

Alignment

ORF - retro_ttru_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.75 %
• Parental protein coverage: 54.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REKPYDVQSLQAALKEVITSRYQLDPKYITNILYENDVIVIDLVQNSSQKTQNDVDIADVAYYFEKDVKD
          REKPY..QSL..ALKEVI.SRYQLDPKYIT..LYENDV...DLVQNS.QK.QNDVDI.DVAYYFEKDV..
Retrocopy REKPYEDQSLYTALKEVIISRYQLDPKYITDVLYENDVLTVDLVQNS-QKIQNDVDIDDVAYYFEKDVNG

Parental  ESLFQSNKMDLRVNGELLDLDPSRTSIYYVDEKPPEFSMQGLQAGIIAVIVVVAVAITAGIAVLVVSRKK
          ESLFQS..M.L.VNGELLDLDP..TSIYYVDEKPPE.S.QGLQAGII.V.VVVA.A.TAGI..LVVSRKK
Retrocopy ESLFQSKRMGLKVNGELLDLDPG*TSIYYVDEKPPELSVQGLQAGIISVVVVVAIAATAGI-MLVVSRKK

Parental  RMAKYEKAEIKEMGEMHREL
          R.AKYEKAE.K.MGE.H.EL
Retrocopy RTAKYEKAEMKDMGEVHWEL

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_394 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_394 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 ,