RetrogeneDB ID: retro_btau_943

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 21:827873..828707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.67498
• Ensembl ID: ENSBTAG00000008306
• Aliases: None
• Description: E3 ubiquitin-protein ligase makorin-1 [Source:RefSeq peptide;Acc:NP_001098449]

Sequence

>retro_btau_943
GCTTCCTCACGCTCCTTGCCTGTGATTGGCTCAGCTGGTGAAAGGGGTTTGTTTGAAGCCACGACAGACAATGCAGGCCT
TGAAGCTGCTGGAGGAGCAGGTGTAGAAGGCTGGGAGAATGCCGTTGAATTTGTTCCTGGGCAACCCTACCGGGGCCGCA
TGGTCCCTTCTGTTTCCGAGGCTCCTGTGCAGAGCTCGATGATTGAGAGGGAACAGATTGTCTTGGGCATGGGGAGGCAG
CTTTGCCGTGATGCTATCGCGGGGCAGTGCTTTCGTGGGCAGAGCTGTATTTATCTCCATGGAGATATATGTGATATGTG
TGGGCTGCCAGTCTTGCACCCCTTGGATGGTGCCCAGAGGGCAGACCATGTAAAGGCCTGCATTGAAGCACACGAAAAGA
ATATGGAGCTCTCTTTTGCCGTGCAGCGCAGTGCGGACAAAGTGTGTGGCATCTGCATGGAGGTTGTCTATGAGAAAGCC
AACCGGAATGATTGCCGCTTTGGCATCCTCTCCAGCTGCAACCACACCTACTGTCTTAAGTGTATCCGCAGGTGGAGAAG
TGCCAGACAATTTGGGAGCAGAGTTATCAAGTCCTGCCCTCAGTGCAGGGTCATGTCCACCTTTGTCATTCCCAGTGAGT
TCTGGGTGGAGGAGGAAGAAGAGAAGCAGAAACTTATTCAGCAGTACTTGGAGGCTTTGAGTCACAAGACCTGCAGGTAT
TTTGGTCGAGGCAGGGTCTGCCCATTTGGAGAGAACTGTTTTTACAAACATGTGTATCCTGAGGGCCAGGGAGAGGAGCC
TCAGCGGCAGGGTGCTGAGGCGTCTGGTACTTGC

Alignment

ORF - retro_btau_943 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.25 %
• Parental protein coverage: 58.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AASSSLSSVGPTVDMNMGEAESRNSNF-ATVGAGSEDWVNAIEFVPGQPYCGRTAPSSAEAPLQGSVTKE
          A.S.SL...G........EA...N....A..GAG.E.W.NA.EFVPGQPY.GR..PS..EAP.Q.S....
Retrocopy ASSRSLPVIGSAGERGLFEATTDNAGLEAAGGAGVEGWENAVEFVPGQPYRGRMVPSVSEAPVQSSMI--

Parental  DAEKEQSAVETKKQLCPYAAVGECRYGENCAYLHGDACDMCGLQVLHPVDAAQRSQHIKSCIEAHEKDME
          ..E.EQ.......QLC..A..G.C..G..C.YLHGD.CDMCGL.VLHP.D.AQR..H.K.CIEAHEK.ME
Retrocopy --EREQIVLGMGRQLCRDAIAGQCFRGQSCIYLHGDICDMCGLPVLHPLDGAQRADHVKACIEAHEKNME

Parental  LSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITS
          LSFAVQRS.D.VCGICMEVVYEKAN....RFGILS.CNHTYCLKCIR.WRSA.QF.S..IKSCP.CR..S
Retrocopy LSFAVQRSADKVCGICMEVVYEKANRNDCRFGILSSCNHTYCLKCIRRWRSARQFGSRVIKSCPQCRVMS

Parental  NFVIPSEYWVEEKEEKQKLIQKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAYPDGRREEPQRQKVGTS
          .FVIPSE.WVEE.EEKQKLIQ.Y.EA.S.K.CRYF..GR..CPFG.NCFYKH.YP.G..EEPQRQ....S
Retrocopy TFVIPSEFWVEEEEEKQKLIQQYLEALSHKTCRYFGRGR-VCPFGENCFYKHVYPEGQGEEPQRQGAEAS

Parental  SRC
          ..C
Retrocopy GTC

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	19.68 RPM
ERP005899_muscle	0.42 RPM	56.80 RPM
SRP017611_brain	0.37 RPM	52.49 RPM
SRP017611_kidney	0.18 RPM	40.48 RPM
SRP017611_liver	0.00 RPM	46.44 RPM
SRP030211_testis	1.07 RPM	588.31 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_943 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_943 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_943 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943 ,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni	ENSCHOG00000011015	3 retrocopies	retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Dasypus novemcinctus	ENSDNOG00000019564	2 retrocopies	retro_dnov_1011, retro_dnov_388,
Erinaceus europaeus	ENSEEUG00000001133	1 retrocopy	retro_eeur_643,
Felis catus	ENSFCAG00000024942	1 retrocopy	retro_fcat_67,
Homo sapiens	ENSG00000133606	4 retrocopies	retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Macropus eugenii	ENSMEUG00000007399	1 retrocopy	retro_meug_1659,
Microcebus murinus	ENSMICG00000002114	1 retrocopy	retro_mmur_1184,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus	ENSMUSG00000029922	1 retrocopy	retro_mmus_2663,
Nomascus leucogenys	ENSNLEG00000001921	4 retrocopies	retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii	ENSOGAG00000009877	2 retrocopies	retro_ogar_3468, retro_ogar_424,
Ochotona princeps	ENSOPRG00000010353	1 retrocopy	retro_opri_1073,
Procavia capensis	ENSPCAG00000014683	1 retrocopy	retro_pcap_19,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes	ENSPTRG00000019766	5 retrocopies	retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa	ENSSSCG00000016498	2 retrocopies	retro_sscr_43, retro_sscr_637,
Tupaia belangeri	ENSTBEG00000004564	2 retrocopies	retro_tbel_1410, retro_tbel_71,
Tarsius syrichta	ENSTSYG00000009996	3 retrocopies	retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus	ENSTTRG00000009528	2 retrocopies	retro_ttru_1064, retro_ttru_1128,