RetrogeneDB ID: retro_btau_1654

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:66280563..66281205(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMNAT1
• Ensembl ID: ENSBTAG00000001361
• Aliases: None
• Description: Nicotinamide mononucleotide adenylyltransferase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q0VD50]

Sequence

>retro_btau_1654
GTTATCATTGCATATCTTGCCACCAAGAATTCAAAGTAGGTGGATGTGGGTGCATGGTAAAAGCTTCAGAAGGAGTGGCT
AGAGACTGCTAAGGTGCTCAGACACCACTGAGAGAAATTGGAGGCTGGTAGCTGTGATCACCAGAAGGACTCACCTATAC
CAGAAAGACCTGAATGGAGGAGGAAGTTGGCTGAACAAAGTCAAGATTTTAGTCAAAAGAAATCCGTGGGGTCAGAAGCA
AAATGTGTGCCAAAGGTAATATTGCTGTGTGGGGCAGATTTATTGGGGTCTTTTGGTGATCCCAACCTGTGGAAGAATGA
GGATTTCACCCAAATTGTAAGAAAGTATGAGCTCATAAGTATTACCCAGGCTGAAACTGTTGTTCAGAAACTCATCTGTG
AAACAGATGTTCTGTGAAAACATCAGAACAACATTCTTCTGGTGAATGAATGGATCACCAATGACATCTTATTCACAAAG
ACCCAGCAAGCCCTCAAAAGGAGTTAGAGCATTCACTATTTGGTACTAGATCTTGTCCAAGAGTATACTGAAAAGCATAA
TTTTTATGACTCCAGGAGCGAAGAGAGGCATTTTGGGGTGATACTGGCTCCTTTGCAAAAAAGCAGTACAGATTCTAAGT
CA

Alignment

ORF - retro_btau_1654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.72 %
• Parental protein coverage: 76.51 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIMAELATKNSKWVEVDTWESLQKEWTETAKVLRHHQEKLEASICDPQQNSPVLEKPGRKRKWAEQKQDI
          VI.A.LATKNSK.V.V..W..LQKEW.ETAKVLRHH.EKLEA..CD.Q..SP..E.P...RK.AEQ.QD.
Retrocopy VIIAYLATKNSK*VDVGAW*KLQKEWLETAKVLRHH*EKLEAGSCDHQKDSPIPERPEWRRKLAEQSQDF

Parental  SEKKSLEQTKTKGVPKVKLLCGADFLESFGVPNLWKSEDITKILGDYGLICITRAGNDAQKFIYESDVLW
          S.KKS......K.VPKV.LLCGAD.L.SFG.PNLWK.ED.T.I...Y.LI.IT.A....QK.I.E.DVL.
Retrocopy SQKKSVG-SEAKCVPKVILLCGADLLGSFGDPNLWKNEDFTQIVRKYELISITQAETVVQKLICETDVL*

Parental  KHQNNIHLVNEWITNDISSTKIRRALRRGQSIRYLVPDLVEEYIEKHNLYSSESEERNVGVVLAPLQRNT
          KHQNNI.LVNEWITNDI..TK...AL.R..SI.YLV.DLV.EY.EKHN.Y.S.SEER..GV.LAPLQ...
Retrocopy KHQNNILLVNEWITNDILFTKTQQALKRS*SIHYLVLDLVQEYTEKHNFYDSRSEERHFGVILAPLQKSS

Parental  TEVKA
          T..K.
Retrocopy TDSKS

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	9.37 RPM
ERP005899_muscle	0.00 RPM	11.09 RPM
SRP017611_brain	0.00 RPM	8.50 RPM
SRP017611_kidney	0.00 RPM	20.69 RPM
SRP017611_liver	0.00 RPM	9.51 RPM
SRP030211_testis	0.00 RPM	15.23 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1654 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1654 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001361	2 retrocopies	retro_btau_1153, retro_btau_1654 ,
Callithrix jacchus	ENSCJAG00000005483	1 retrocopy	retro_cjac_1690,
Homo sapiens	ENSG00000173614	3 retrocopies	retro_hsap_247, retro_hsap_2740, retro_hsap_2989,
Macaca mulatta	ENSMMUG00000005863	2 retrocopies	retro_mmul_1488, retro_mmul_446,
Nomascus leucogenys	ENSNLEG00000009375	2 retrocopies	retro_nleu_1072, retro_nleu_741,
Oryctolagus cuniculus	ENSOCUG00000023212	1 retrocopy	retro_ocun_1243,
Otolemur garnettii	ENSOGAG00000033037	2 retrocopies	retro_ogar_1088, retro_ogar_637,