RetrogeneDB ID: retro_btau_1331

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:94117643..94118837(+)
• Located in intron of: ENSBTAG00000001754

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF512
• Ensembl ID: ENSBTAG00000003902
• Aliases: None
• Description: Zinc finger protein 512 [Source:UniProtKB/Swiss-Prot;Acc:A4FV61]

Sequence

>retro_btau_1331
ATGTCTTCCAGACTCCGTGCAGTGCCCGCTACCCCGGGACCCACACCCTTTAAGCAGCAGAGAAGCACGAGGATCATGGA
AGCTAAGAATAGCAGAACCCAATCCTCCATAAAGGATAAGAGTTTCCAGTACACTATCCCTCATGATGACTCCTTAAGCG
GTTCATCATCTGCTTCATGAACCAGGGAGTGATTTTCTAGCATCCTTCTGAAAATCTACCTACAGGGTGAAGATGAGAAG
GATCAAGTCAGCTGCTGCTTCCCATGTAGAAGGGTCAGATGGAATATCAACCAAAGGAAAAAGGAAACCCAGGCAGGAAG
AAGATGAAGACTATCAGAGAATTTCCACAGAAGAAGCATAAGCTTTATGGGAGGAAGCAGCAGCCTAAAGCTCAGCCTAA
TCCCAAAGCCCAGACTCACCGTATTTGGAAGGAACCACCGGCTTATGCAGCAGGCAGTTTAGAGGAACAGTGGTACTTAG
AAATTGTGAATGAAGGCAGTGTCTCCTGTCCTACCTGCCAGGCAGTAGGGAGAAAGACCATAGAGGGCTTAAAGAAACAC
AGGGAAACTGTAAATAGGAAATGTTTACCTGTCGTCATTGTGGGAAACAGCTTCTTTCACTAGCAGAGATGAAGTATCAT
GTCATGGCAAATCATAATAGCTTCCCCATTTTAAGGCTGGAGATGAAATAGATGAGCCAAGTGAGAGGGAACGTCTCTGA
ACAGTTCTCAAGAAACTGGGAAAGCTGAGATGCATGCATGAGAGTTGCTCTAGTAGCTTCACCAGCATCATGGGATATCT
GTACCATGTGAGAAAATGAGCAAAGGGGCTGCTGAGCTGGAGAAGATGACCCTGAAATGTCACCACTGTGGAAAGCTGTA
TAGATTGAAGACTGGACTCGTATATCACTTGTATATAAGAGCATAGTACTGTATTCTTCTTTCCAGAGTCAGGACAGCCA
GAGTGCTTGAAGGACATGAGCTTGGAGTCAAAGAGTGGAGACCGAGTTCAGAGGCAGATAGCTGTGTACCACCTGCAGGA
ACTGGCTTCTGATGAACTGGCCAAGGAATGGCCTGAGAGAAAGGTGCTTCAGGATCTGGTACCTGATGATTGGAAGTTAA
AATATACTTGTCCTGGGCTACTGACCTTCAGCCAAGAAGTACTACACAAATAGAAGTCAGAAGTATCATCGCAT

Alignment

ORF - retro_btau_1331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.62 %
• Parental protein coverage: 71.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MSSRLGAVPATPGPTPFKQQRSTRIVGAKNSRTQCSIKDNSFQYTIPHDDSLSGSSSASSC-EPVSDFPA
          MSSRL.AVPATPGPTPFKQQRSTRI..AKNSRTQ.SIKD.SFQYTIPHDDSL..S.S.S...EP.SDF.A
Retrocopy MSSRLRAVPATPGPTPFKQQRSTRIMEAKNSRTQSSIKDKSFQYTIPHDDSL--SGSSSAS>EPGSDFLA

Parental  SFRKSTYWMKMRRIKSAAASHVEGPGGVSTKGKRKPRQEEDEDY-REFPQKKHKLYGRKQRPKAQPNPKA
          SF.KSTY..KMRRIKSAAASHVEG..G.STKGKRKPRQEEDEDY.REFPQKKHKLYGRKQ.PKAQPNPKA
Retrocopy SF*KSTYRVKMRRIKSAAASHVEGSDGISTKGKRKPRQEEDEDY>REFPQKKHKLYGRKQQPKAQPNPKA

Parental  QTRRIRKEPPAYAAGSLEEQWYLEIVDKGSVSCPTCQAVGRKTIEGLKKHME-NCKQEMFTCHHCGKQLR
          QT.RI.KEPPAYAAGSLEEQWYLEIV..GSVSCPTCQAVGRKTIEGLKKH.E.NCK.EMFTC.HCGKQL.
Retrocopy QTHRIWKEPPAYAAGSLEEQWYLEIVNEGSVSCPTCQAVGRKTIEGLKKHRE<NCK*EMFTCRHCGKQLL

Parental  SLAGMKYHVMANHNSLPIL-KAGDEIDEPSERERLRTVLKRLGKLRCMRESCSSSFTSIMGYLYHVR-KC
          SLA.MKYHVMANHNS.PIL.KAGDEIDEPSERERL.TVLK.LGKLRCM.ESCSSSFTSIMGYLYHVR.K.
Retrocopy SLAEMKYHVMANHNSFPIL<KAGDEIDEPSERERL*TVLKKLGKLRCMHESCSSSFTSIMGYLYHVR<KM

Parental  GKGAAELEKMTLKCHHCGKPYRSKAGLAYHLRS-EHGPISFFPESGQPECLKDMSLESKSGGRVQRRSAK
          .KGAAELEKMTLKCHHCGK.YR.K.GL.YHL...EH....FFPESGQPECLKDMSLESKSG.RVQR....
Retrocopy SKGAAELEKMTLKCHHCGKLYRLKTGLVYHLYI>EHSTVFFFPESGQPECLKDMSLESKSGDRVQR---Q

Parental  IAVYHLQELASAELAKEWPKRKVLQDLVPDDRKLKYTRPGLPTFSQEVLHKWKSDIKKY
          IAVYHLQELAS.ELAKEWP.RKVLQDLVPDD.KLKYT.PGL.TFSQEVLHK.KS.....
Retrocopy IAVYHLQELASDELAKEWPERKVLQDLVPDDWKLKYTCPGLLTFSQEVLHK*KSEVSSH

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	8.22 RPM
ERP005899_muscle	0.16 RPM	20.48 RPM
SRP017611_brain	0.00 RPM	37.23 RPM
SRP017611_kidney	0.12 RPM	27.26 RPM
SRP017611_liver	0.00 RPM	8.15 RPM
SRP030211_testis	0.03 RPM	38.53 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1331 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1331 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1331 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003902	1 retrocopy	retro_btau_1331 ,
Echinops telfairi	ENSETEG00000015916	1 retrocopy	retro_etel_913,
Sorex araneus	ENSSARG00000002246	1 retrocopy	retro_sara_503,
Sarcophilus harrisii	ENSSHAG00000014564	1 retrocopy	retro_shar_808,
Tarsius syrichta	ENSTSYG00000006511	1 retrocopy	retro_tsyr_1021,