RetrogeneDB ID: retro_btau_1706

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:60278086..60280369(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UTP14A
• Ensembl ID: ENSBTAG00000013671
• Aliases: UTP14A, UTP14C
• Description: U3 small nucleolar RNA-associated protein 14 homolog A [Source:UniProtKB/Swiss-Prot;Acc:Q3T0Q8]

Sequence

>retro_btau_1706
ATGAGCGCGAACCAGGTTGCGGAGAACAATCTTCTGGCTTCGAACCAACAGAATGAACTAGAGGATTTGCCAAAAGACTA
CCCCTTGAGCACCAGTGAAGATGAAGGGGACAAAGATGGAGAAAGAAAGCATCAGAAGCTTCTGGAATCAATCAATTCAC
TTAATGGAAAGGATAGGCAGAAATTGGCTGAGAGGTCAGAGGCTAGTCTGAAGGTGTCAGAGTTCAGTGTAAGTTCTGAA
GAATCAGGAGAAAAGCTGGTCCTTTCAGATCTGCTTGAGCCTGTTAAAACTTCATCCTCATTGGCTGCTGTGAAAAAGCA
GCTAAATTGAGTGAAATTGAAGAAGACTGTGGAGTTACCACTTCACAGAGAAGAGATTGAGCGGATCCACAGAGAAGTGG
CATTCAATAAAAGCTCCCAAATCCTCTCCAAATGGGATCCTGTCGTTCTGAAGAACTGGCAAGCAGAGCGGCTGGTTTTT
CCCCTGAGCAAGCCCCAATCAGCCTTTGCGTCCATCGAACACGTGGTCAGTGGCTGGAAGGCAGGAACTACCCTGGAGCA
GAAGATTTTAAATCTTCTCCATAAGAACAAGCAGCCCGTGACAGACCCTTTACTGACTCCCATGGAAAAGGCCTCTCTCA
AAGCTATGAGCCTGGAAGAGGTAAAGATGCGCCGAGCAGAGCTTCAAAGGACCTGGGCCCTGCAATCCTACTACGAGGCC
AGGGCTCAAAGAAAGAAGAGAATCAAAAGCAAAAAGTATCACAGAATTCTGAAGAAAGGAAAGGCCAAGCAAGCCTTAAA
AGATTTTGAGAAGCTGCAGAAGGTCAATCCTGGTGCAGCACTAGAAGAACTAGAAAAACTTGACAAGGCCAGAATGATGG
AGCGAATGAGCCTTAAGCACCAGAACAGTGGGAACTGGGCAAAATCAAAGGCAATTATGGCCAAATATGACCTGGAGGCT
CACCAGGCTATACAGGAACAGCTGGCCAGGAACAAAGAGCTGACGCATAAGGTCCAGGCGGCCTCTGAGAGTGAGGAAGA
GGAGGAAGGCCAGGAGGAAGAGTCAGAACCTCTTGTCCCTGACATGGTGAATGGGGTGCAGATAAAGGCAAATGGACTGA
ATCCCTGATGTTCCGGAATCACTTCATTGATGCCGAAGAGGCTGAGGTCCAAAAAGACCTGGAGGATCCTGCTGAGCCTG
AAGCCCAGGAGACTTCTGAAAGTGAGGAAGAAACTCTCTTGAAAGAATTTGAGGAAAGGCGATCACTTAGACAGAAGTCT
GAGCTCAACCACATGGCAGAGCCAGCGCACAGATGTGTAACAAAGGATCCTTAGCAGCCAGGAGGTACTGTCCGAATTGA
GGGCACTGTCTCAGAAACTCATCACGGAGAACCATCAGTCAGGGAAGCAAGAACTGAGTTCAGCGAGGACTGCTCAGAGA
GAGGAACCTGCCAGGGAGGAAGAGGAGCCCATGTTGCTGCAGAGGCCAAAGAGAGCTCGGACTCTGGACGAGCTGGAGGA
GCTGGGCAGAGAAGGGTGTGTTGAAAACAAGGAGCTTCCCAGAACTGCAGTGGAAGGGCTGCAGTTGGAGAAGAATCTAA
GTAATCATATTGGCGCCCCCAAGGAGAAGAAAAGGAAGGAGCAAATGATTGATCTCCAGAACCTCCTAACCACAAAATCG
CCTTCTGTGAAGTCCTTGGTAGTTCCCATGACTGTACAGGCGTTGGAAGATGAAGAAGAGAGAGATCAAAGGCAGATAAT
AAAGGAAGCTTTTGCTGGGGATGATGTCATCAGAGACTTATTGAAAGAGAAGAGGGAAGCCGTGGAGGCGAGTAAGCCAA
AGGACCTGGACCTGACTCTGCCTGGCTGGAGCGAGTAGGGTGGTATGGGCCTGAAGCCCAGCGCCAAGAAGAGACGCCCG
TTTCTCATTAAAGCCCCTGAGGGTCCTCTGAGGAAAGACAAGAATCTGCCAAACGTGATTATCAATGAGAAGCGGAACAG
CCATGCAGCAGCTCATCAGGGGCAGGTGTTTCCGCATCCATTCACACACCATCAACAATTTGAAAGGACCATCCAGACCC
CCATAGGATCTACATGGAACACCCAGAGGGCCTTCCAAAAGCTGACCATGCTCAAGGTTGTCACCAATCCAGGCCATATC
ATTAAGCCTATCAATACAGAGGATGTGGGCTGCTGGTCTTCCTCAGGGTCGGACCTCTGTCGTACAGAGGAATCCAAAAC
AACTCTCTATACGTCACAAAAAACATCTGGAGAATAACTGTGT

Alignment

ORF - retro_btau_1706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.53 %
• Parental protein coverage: 99.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNANQAAESNLLASNQQKELEDLPKDYPLSTSEDEGDKDEERKHQKLLESISSLNGKDRQKLADRSEASL
          M.ANQ.AE.NLLASNQQ.ELEDLPKDYPLSTSEDEGDKD.ERKHQKLLESI.SLNGKDRQKLA.RSEASL
Retrocopy MSANQVAENNLLASNQQNELEDLPKDYPLSTSEDEGDKDGERKHQKLLESINSLNGKDRQKLAERSEASL

Parental  KVSEFSVSSEGSGEKLVLSDLLEPVKTSSSLAAVKKQLNRVKSKKTVELPLHREEIERIHREVAFNKSSQ
          KVSEFSVSSE.SGEKLVLSDLLEPVKTSSSLAAVKKQLN.VK.KKTVELPLHREEIERIHREVAFNKSSQ
Retrocopy KVSEFSVSSEESGEKLVLSDLLEPVKTSSSLAAVKKQLN*VKLKKTVELPLHREEIERIHREVAFNKSSQ

Parental  ILSKWDPVVLKNRQAEQLVFPLSKPQSAFAPIEHVVNGWKAGTPLEQEIFNLLHKNKQPVTDPLLTPVEK
          ILSKWDPVVLKN.QAE.LVFPLSKPQSAFA.IEHVV.GWKAGT.LEQ.I.NLLHKNKQPVTDPLLTP.EK
Retrocopy ILSKWDPVVLKNWQAERLVFPLSKPQSAFASIEHVVSGWKAGTTLEQKILNLLHKNKQPVTDPLLTPMEK

Parental  ASLKAMSLEEVKMRRAELQRARALQSYYEARARREKRIKSKKYHRILKKGKAKQALKDFEKLQKVNPAAA
          ASLKAMSLEEVKMRRAELQR..ALQSYYEARA.R.KRIKSKKYHRILKKGKAKQALKDFEKLQKVNP.AA
Retrocopy ASLKAMSLEEVKMRRAELQRTWALQSYYEARAQRKKRIKSKKYHRILKKGKAKQALKDFEKLQKVNPGAA

Parental  LEELEKLDKARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLARNKELTQKVRAASESEEEGEG
          LEELEKLDKARMMERMSLKHQNSG.WAKSKAIMAKYDLEA.QA.QEQLARNKELT.KV.AASESEEE.EG
Retrocopy LEELEKLDKARMMERMSLKHQNSGNWAKSKAIMAKYDLEAHQAIQEQLARNKELTHKVQAASESEEEEEG

Parental  QEEEEEPLVPDLVNEVQIKANGLNP-WMFRNHFIDAKEAEVQKDLEDPAEPEAQETSESEEEKAVVEEET
          QEEE.EPLVPD.VN.VQIKANGLNP..MFRNHFIDA.EAEVQKDLED...P...E..E..E.....EEET
Retrocopy QEEESEPLVPDMVNGVQIKANGLNP<LMFRNHFIDAEEAEVQKDLED---PAEPEAQETSES----EEET

Parental  LLKEFEERRSLRQKSELNHMAEPVHRRVTKDP-SSQEVLSDLRALCQKLRTENHQSGKQELSSARTAQRE
          LLKEFEERRSLRQKSELNHMAEP.HR.VTKDP.SSQEVLS.LRAL.QKL.TENHQSGKQELSSARTAQRE
Retrocopy LLKEFEERRSLRQKSELNHMAEPAHRCVTKDP>SSQEVLSELRALSQKLITENHQSGKQELSSARTAQRE

Parental  EPAREEEEPMLLQRPERARTLDELEELGREGCVENEELPRTAVEGLQLEKNLSNHIGAPKEKKRKEQMID
          EPAREEEEPMLLQRP.RARTLDELEELGREGCVEN.ELPRTAVEGLQLEKNLSNHIGAPKEKKRKEQMID
Retrocopy EPAREEEEPMLLQRPKRARTLDELEELGREGCVENKELPRTAVEGLQLEKNLSNHIGAPKEKKRKEQMID

Parental  LQNLLTTKSPSVKSLAVPTTVQELEDEEERDQRQIIKEAFAGDDVIRDFLKEKREAVEASKPKDLDLTLP
          LQNLLTTKSPSVKSL.VP.TVQ.LEDEEERDQRQIIKEAFAGDDVIRD.LKEKREAVEASKPKDLDLTLP
Retrocopy LQNLLTTKSPSVKSLVVPMTVQALEDEEERDQRQIIKEAFAGDDVIRDLLKEKREAVEASKPKDLDLTLP

Parental  GWGEWGGIGLKPSAKKRRRFLIKAPEGPPRKDKNLPNVIINEKRNTHAAAHQVQVLPHPFTHHQQFERTI
          GW.E.GG.GLKPSAKKRR.FLIKAPEGP.RKDKNLPNVIINEKRN.HAAAHQ.QV.PHPFTHHQQFERTI
Retrocopy GWSE*GGMGLKPSAKKRRPFLIKAPEGPLRKDKNLPNVIINEKRNSHAAAHQGQVFPHPFTHHQQFERTI

Parental  QTPVGSTWNTQRAFQKLTMPKVVTKPGHIIKPIKAEDVGYRSSSRSDLSVVQRNPKRLSIRHKKHLENNC
          QTP.GSTWNTQRAFQKLTM.KVVT.PGHIIKPI..EDVG..SSS.SDL.........L....K...E..C
Retrocopy QTPIGSTWNTQRAFQKLTMLKVVTNPGHIIKPINTEDVGCWSSSGSDLCRTEESKTTLYTSQKTSGE*LC

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	40.59 RPM
ERP005899_muscle	0.05 RPM	178.16 RPM
SRP017611_brain	0.05 RPM	71.90 RPM
SRP017611_kidney	0.00 RPM	81.74 RPM
SRP017611_liver	0.08 RPM	31.94 RPM
SRP030211_testis	0.62 RPM	8.90 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1706 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1706 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1706 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706 ,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,