RetrogeneDB ID: retro_btau_66

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:88032647..88033607(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000004381
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSBTAG00000006474
• Aliases: EPCAM, TACSTD1
• Description: epithelial cell adhesion molecule precursor [Source:RefSeq peptide;Acc:NP_001030367]

Sequence

>retro_btau_66
ATGGCCCGGGGCCCGGGCCTCGCGCTGCTGTCGCCGTGGCTCCTGATGCTGGCGGCGGTGATCGGCCACGCGGCCGCGCA
GAACCAGTGCGTGTGTCCCACCAACAAGATGACCGTGTGCGACGAGCGCGACCCGAGCGGCCGCTGCCAGTGCCGCGTGC
TCGGCTCGAACCAGGCGGTCAACTGTTCCACGCTCACGTCCAAGTGCCTGCTGCTCAAGGCGCGCATGAGCGCCTCCCAC
AGCGGCCGCGCGCTGGTGCGGCCGAGCGAGCACGCGATCGTGGACAACGACGGCCTGTACGACCCGGACTGCGACCAGCA
GGGGCGCTTCAAGGCGCGCCAGTGCAACCAGACGTCGGTGTGCTGGTGCGTGAACTCGGTGGGCGTGCGCCGCACCGACA
AGGGCGACCTGAGCCTGAAGTGCGACGAGGTGGTGCGCACCTACCACATCCTTATTGACCTGCGCCACCGCCCGGACGCC
CCAGCCTTCAACCACTCGGACCTGGACGCTGAGCTGCGGCAGCTCTTCCAGCAGCGCTATCTGCTGCAGCCCAAGTTCGT
GAGTGCTGTGCACTACGAGCACCCTACCATCCAGATCGAGCTGCGCCAGAACTCGTCGCAGAAGGTCGCCGGCGAGGTGG
ACATCGGCGACGCCGCGTACTACTTCGAGAGGGACGTCAAGGGCGAGTCGCTGTTCCTAGGCCCCCGCGACCTCAACTTG
CGCGTGGGCGGACAGCCCCTGGTCCTGGAGCAGATGCTCATCTACTACCTGGACGAGAAGCCCCCCCAGTTCTCCATGAA
GCGCCTCACCAGCGGCCTCATCGCCGTCGTCGTGGTGGTCGTGGTGGCGGTGGTCGCCGGCGCGGCCGTCCTGGTGATCA
CCAATCGCAGAAAGTCGGGAAAGTACAAGAAGGTGGAGATCAAGGAACTGGGGGAGATAAGACAGAAACCGAGCTTGTAG

Alignment

ORF - retro_btau_66 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.16 %
• Parental protein coverage: 95.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLVAAATAAVAAAQEGCVCENYKLTTNCSVNALGQCQCTSVGTQHSVICTKLATKCLVMKAEISHSKSGR
          LL..AA....AAAQ..CVC...K.T........G.CQC...G....V.C..L..KCL..KA..S.S.SGR
Retrocopy LLMLAAVIGHAAAQNQCVCPTNKMTVCDERDPSGRCQCRVLGSNQAVNCSTLTSKCLLLKARMSASHSGR

Parental  R--RKPEGAIQNNDGLYDPECDDKGLFKAKQCNGTSTCWCVNTAGVRRTDK-DSEISCSEPVRTYWIIIE
          ...R..E.AI..NDGLYDP.CD..G.FKA.QCN.TS.CWCVN..GVRRTDK.D....C.E.VRTY.I.I.
Retrocopy ALVRPSEHAIVDNDGLYDPDCDQQGRFKARQCNQTSVCWCVNSVGVRRTDKGDLSLKCDEVVRTYHILID

Parental  LKHKTREKPYDLQSLQSALKDVITNRYQLDPKYITNILYENDVITIDLVQNSSQKTQNDVDIADVAYYFE
          L.H...........L...L......RY.L.PK......YE...I.I.L.QNSSQK....VDI.D.AYYFE
Retrocopy LRHRPDAPAFNHSDLDAELRQLFQQRYLLQPKFVSAVHYEHPTIQIELRQNSSQKVAGEVDIGDAAYYFE

Parental  KDVKDESLFHSKR-MDLRVNGELLDLDPGRTSIYYVDEKPPEFSMQGLQAGIIAVIVVVVVAIIAGIIVL
          .DVK.ESLF...R...LRV.G..L.L......IYY.DEKPP.FSM..L..G.IAV.VVVVVA..AG..VL
Retrocopy RDVKGESLFLGPRDLNLRVGGQPLVLE--QMLIYYLDEKPPQFSMKRLTSGLIAVVVVVVVAVVAGAAVL

Parental  VVSRKKSMTKYEKAEIKEMGEMHRE
          V........KY.K.EIKE.GE....
Retrocopy VITNRRKSGKYKKVEIKELGEIRQK

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
ERP005899_liver	0.00 RPM	25.38 RPM
ERP005899_muscle	0.26 RPM	689.00 RPM
SRP017611_brain	0.09 RPM	4.43 RPM
SRP017611_kidney	2.02 RPM	159.44 RPM
SRP017611_liver	0.00 RPM	7.40 RPM
SRP030211_testis	0.26 RPM	97.42 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_btau_66 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CN434363	88032638	88032888	100	250	0	250
DN638769	88032783	88033109	99.7	325	1	324
DN639026	88032888	88033109	99.6	220	1	219

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_66 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_66 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_92
Macaca mulatta	retro_mmul_34
Callithrix jacchus	retro_cjac_3006
Sus scrofa	retro_sscr_69

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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,