RetrogeneDB ID: retro_btau_1539

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:66926604..66927249(+)
• Located in intron of: ENSBTAG00000005800

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.28556
• Ensembl ID: ENSBTAG00000014476
• Aliases: None
• Description: adenosine deaminase-like protein [Source:RefSeq peptide;Acc:NP_001069045]

Sequence

>retro_btau_1539
ATGATGGAGGCGGAAGACAAACAGCAGCCCTGGAAGACAATCTTTCCCTTGGAATTACCTAAAATGGAACTTCATTTTCA
TCTGAGTGGATCCATTAGTTCTAATGCCATGAGGAAATTAGTACACAATAAACCAGGTCTTAAAATCCATGACTAGATGA
CTATGATTAACAAGGGAAAGAAAAGAACTTTGGAGGAATGTCTCCAAAAGTTTCAAAGTATTCATCAGCTTGCTACTGAA
GAGATGTTCATGGCCACAAGAGATGTTATTAAAGAATTCACAGATGATGGTGTCAAGTGCCTGAAACAAAGGAACACACC
CAGAAAAGAAACTACGGAATGACTGAAAAGACTTATGTGGAATTTGTACTTGATACTATAAAACAGTCTGAAAAAAGAGA
ACAGAGACACTGATGTTAGGTATTTGACAGCAATCAACAGAAGAGGTGGCCCTTCAGTAGCCGAGGAGACTGTTAAGCTT
CCTGAGGAGTTCTTCCTTTCTACTGAGGACACAGTTCTTGGGTTTGACCTCAGTGGAAACCCTATGGTAGGACAAACAAT
ATTCCTTGGAACTTTTTTAGAACCTGATAAAACATATCTTCATTTGCCATTACATTTTACAGAGATCCCAAAGCAAAAAA
CTGAA

Alignment

ORF - retro_btau_1539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.71 %
• Parental protein coverage: 61.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMEAEE--QPWKTTFYSKLPKVELHAHLNGSISSSTIRKLIAKKPDLKIHDQMTMIDKGEKRTLEECLQM
          MMEAE...QPWKT.F...LPK.ELH.HL.GSISS...RKL...KP.LKIHD.MTMI.KG.KRTLEECLQ.
Retrocopy MMEAEDKQQPWKTIFPLELPKMELHFHLSGSISSNAMRKLVHNKPGLKIHD*MTMINKGKKRTLEECLQK

Parental  FQIIHLLTTTPEDVLMVTKDVIKEFADDGVKYLELRSTPRGEDAT-GMTKKTYVESILEGIKQS-KEENV
          FQ.IH.L.T..E...M.T.DVIKEF.DDGVK.L..R.TPR....T.GMT.KTYVE..L..IKQS.K.EN.
Retrocopy FQSIHQLAT--EEMFMATRDVIKEFTDDGVKCLKQRNTPR-KETT<GMTEKTYVEFVLDTIKQS>KKENR

Parental  DIDVRYLISIDRRGGSSAAKEAVKLAEEFFLSAEDTVLGLDLSGDPSAGQAKDFLEPLLEAKKSGLKLAL
          D.DVRYL..I.RRGG.S.A.E.VKL.EEFFLS.EDTVLG.DLSG.P..GQ...FL...LE..K..L.L.L
Retrocopy DTDVRYLTAINRRGGPSVAEETVKLPEEFFLSTEDTVLGFDLSGNPMVGQT-IFLGTFLEPDKTYLHLPL

Parental  HLSEIPNQKTE
          H..EIP.QKTE
Retrocopy HFTEIPKQKTE

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	10.24 RPM
ERP005899_muscle	0.00 RPM	8.92 RPM
SRP017611_brain	0.00 RPM	4.43 RPM
SRP017611_kidney	0.00 RPM	7.94 RPM
SRP017611_liver	0.00 RPM	5.21 RPM
SRP030211_testis	0.02 RPM	3.84 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1539 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1539 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_530

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014476	1 retrocopy	retro_btau_1539 ,
Cavia porcellus	ENSCPOG00000002337	1 retrocopy	retro_cpor_1193,
Oryctolagus cuniculus	ENSOCUG00000024818	2 retrocopies	retro_ocun_1237, retro_ocun_85,
Sus scrofa	ENSSSCG00000004710	1 retrocopy	retro_sscr_530,