RetrogeneDB ID: retro_btau_1358

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:87914161..87914896(-)
• Located in intron of: ENSBTAG00000005110

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.29416
• Ensembl ID: ENSBTAG00000022920
• Aliases: None
• Description: E3 ubiquitin-protein ligase RNF128 precursor [Source:RefSeq peptide;Acc:NP_001069539]

Sequence

>retro_btau_1358
ACATGGCTCGCTCTTGTCGAACGGGGAGGCTGTACCTTCACCCAGAAGATCAAGGTGGCGGTGGAGAATGGAGCCAGTGG
AGTGATCATCTATAACTTTCCAGGAACTGGCAATCAGGTCTTTCCCATGTCTCATCAGATATTTGAAGACATCGTTGTGG
TGATGATTGGTAACTTAAAAGGCATGGAGATTTTGCATTTAATTCAGAAGGGTGTTCATGTGACCGTCACGATTGAGGTG
GGAAGAAAACACATCATCTGGATGAATCACTATTTTGTCTCTTTTGTGATCGTCACAACCGCTACGTTAGTGTATTTCAT
CTTTTATCATATTCGAAGACTTTGGGTAGCAAGGGTTCAGAACCGGAGGTGGCAGCGGTTAACAAATGATCTCAAGAAAG
CATTTGGCCAGCTTCAGGTTCGGGTACTGAAAGAGGGGGACGAGGAAGTAAGCGGCAATGGAGATAGCTGCGTAGTTTGC
TTTGAACTCTATAAGCCTAACGATACAATTCGTGTTCTGACCTGTAAACATTTTTTCCACAAGAATTGCATTGACCCCTG
GATCTTAGCCCATGGGACATGCCCCATGTGCAAATGTGATATTCTTAAAGCTTTGGGGATTCAGATGGATGTTGAAGATG
GAACAGAGTCTTTGCAAGTTTTAATGTCCAACGAATTGGCTGATATCCTGTCATCTAGTGAAGAGGGCACAAATAATGAA
CTTCCTCCTTCAGGA

Alignment

ORF - retro_btau_1358 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.36 %
• Parental protein coverage: 58.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQSIQ
          .WLAL..RGG.CTF..KI..A.E.GASG..I.NFPGT.N.V.PMSH....DIV..MIGNLKG..IL..IQ
Retrocopy TWLALVERGG-CTFTQKIKVAVENGASGVIIYNFPGTGNQVFPMSHQIFEDIVVVMIGNLKGMEILHLIQ

Parental  RGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
          .G..VT..IEVG.KH..W.NHY...FV.V.....TA..V.YFIFY..RRL..AR.Q.R....L..D.KKA
Retrocopy KGVHVTVTIEVGRKHIIWMNHYFVSFVIVT----TATLV-YFIFYHIRRLWVARVQNRRWQRLTNDLKKA

Parental  IGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHVFHKTCVDPWLLEHRTCPMCKCDILKA
          .G.LQ.R.LK.GD.E....GDSC.VC.ELYKPND..R.LTC.H.FHK.C.DPW.L.H.TCPMCKCDILKA
Retrocopy FGQLQVRVLKEGDEEVSGNGDSCVVCFELYKPNDTIRVLTCKHFFHKNCIDPWILAHGTCPMCKCDILKA

Parental  LGIEVDVEDGSVSLQVPVSNETSSNASPHEEDNRSETASSG
          LGI..DVEDG..SLQV..SNE.....S..EE....E...SG
Retrocopy LGIQMDVEDGTESLQVLMSNELADILSSSEEGTNNELPPSG

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	0.29 RPM	692.77 RPM
ERP005899_muscle	0.16 RPM	139.26 RPM
SRP017611_brain	0.00 RPM	17.91 RPM
SRP017611_kidney	0.06 RPM	133.84 RPM
SRP017611_liver	0.00 RPM	190.73 RPM
SRP030211_testis	38.18 RPM	10.97 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1358 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1358 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2651
Oryctolagus cuniculus	retro_ocun_37
Sus scrofa	retro_sscr_597

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004913	1 retrocopy	retro_btau_217,
Bos taurus	ENSBTAG00000022920	1 retrocopy	retro_btau_1358 ,
Loxodonta africana	ENSLAFG00000002816	1 retrocopy	retro_lafr_946,
Macropus eugenii	ENSMEUG00000001567	1 retrocopy	retro_meug_1139,
Mustela putorius furo	ENSMPUG00000003695	1 retrocopy	retro_mputfur_340,
Oryctolagus cuniculus	ENSOCUG00000012328	1 retrocopy	retro_ocun_37,
Pan troglodytes	ENSPTRG00000022151	1 retrocopy	retro_ptro_2651,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Ictidomys tridecemlineatus	ENSSTOG00000022922	2 retrocopies	retro_itri_1254, retro_itri_1255,
Tursiops truncatus	ENSTTRG00000007536	1 retrocopy	retro_ttru_6,