RetrogeneDB ID: retro_btau_1752

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:85444510..85445476(+)
• Located in intron of: ENSBTAG00000012861

Retrocopy information

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

Parental gene information

• Parental gene symbol: IKZF5
• Ensembl ID: ENSBTAG00000023847
• Aliases: None
• Description: Zinc finger protein Pegasus [Source:UniProtKB/Swiss-Prot;Acc:A4IFJ6]

Sequence

>retro_btau_1752
ATGAGTGAAAAGAAACCAGAGCCTTTGGACTTCATGAAAGATTTTCAGGAATTCCTGACTCAGCAGACTCATCATGTCAA
CATGATTTCTGGATCAGTTAGTGGGGACAAAGAAGCAGAGGCTCTTCAGGGAGCTGGAACAGATGGTAATCAAAATGGAA
TCAATCCCCCATCTGTTGAAGTTTCCTTGGATGAAAACTCAGGAATGTTAGTAAATGGGTTTGAAAGGACCTTTGATGGA
AAGCTCAAGTGTTGATACTGCAACTATGCCAGCAAAGGCACCACCTGGCTCACTGAACACATTTAAATCCACACAGGTGA
GAAACTTCAGTGATGTCACTTATGCCCATTTGCATCTGCCTATGATCGTCATCTGGAAGCCCATATGTGTTCCCATATAG
GAGAAAAACCACACAAATGTGGATTGTGTTCCTTTTGCTGCAGTGACTGAAGCATCCTGTCCCATCATCAAAAGCACAAA
TCTAAAATGGTATTAGGTTAAAGGTACTAGGTCTTCCTTAAGCAGCAAGAGAATGTGCAGGGGTTTACAGAAGAAAATTA
GCAATCTGAGCTATAGCAGAAGAGCACTAATCAACTTAAGCCCACCTTCCACAGTGGTTCAGGAGCCAGACTGCCTTAAT
GATTTTACCTATGAAATCCCAAACATCCAGAGTGACTTCTATGAAAGCATGGCAAAACCCACACCAACAGGGGGCCTGCC
AAGAGACCCCCAAGAACTCATGGTTGACAACCCATTAAACCAGCTCTCAACTCTAGCAGGACAATTGTCCAGTTTGCCAC
TTGAAAACCAAAACCTCGCACCCCCTGATGTAGTTCCCTGCACCAAGAAGAAGCCTTTCTCTGATGCAGCAGCCCTCTAC
CCAGGCAGTAGTTTTTGTAGTGTTGGCAAGTATCCCTTAGAGTTCCTCTTCCTACCAGCCCTGAACCTCAGCCGTCACAG
TCAGAG

Alignment

ORF - retro_btau_1752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.94 %
• Parental protein coverage: 76.61 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGEKKPEPLDFVKDFQEYLTQQTHHVNMISGSVSGDKEAEALQGAGTDGDQNGLDHPSVEVSLDENSGML
          M.EKKPEPLDF.KDFQE.LTQQTHHVNMISGSVSGDKEAEALQGAGTDG.QNG...PSVEVSLDENSGML
Retrocopy MSEKKPEPLDFMKDFQEFLTQQTHHVNMISGSVSGDKEAEALQGAGTDGNQNGINPPSVEVSLDENSGML

Parental  VDGFERTFDGKLKCRYCNYASKGTARLIEHIRIHTGEKPHRCHLCPFASAYERHLEAHMRSHTGEKPYKC
          V.GFERTFDGKLKC.YCNYASKGT..L.EHI.IHTGEK...CHLCPFASAY.RHLEAHM.SH.GEKP.KC
Retrocopy VNGFERTFDGKLKC*YCNYASKGTTWLTEHI*IHTGEKLQ*CHLCPFASAYDRHLEAHMCSHIGEKPHKC

Parental  ELCSFRCSDRSNLSHHRRRKHKMVP-IKGTRSSLSSKKMWGVLQKKTSNLNYSRRALINLSPPSMVVQKP
          .LCSF.CSD.S.LSHH...K.KMV...KGTRSSLSSK.M...LQKK.SNL.YSRRALINLSPPS.VVQ.P
Retrocopy GLCSFCCSD*SILSHHQKHKSKMVL>VKGTRSSLSSKRMCRGLQKKISNLSYSRRALINLSPPSTVVQEP

Parental  DYLNDFTHEIPNIQTDSYESMAKTTPTGGLPRDPQELMVDNPLNQLSTLAGQLSSLPPENQNPASPDVVP
          D.LNDFT.EIPNIQ.D.YESMAK.TPTGGLPRDPQELMVDNPLNQLSTLAGQLSSLP.ENQN.A.PDVVP
Retrocopy DCLNDFTYEIPNIQSDFYESMAKPTPTGGLPRDPQELMVDNPLNQLSTLAGQLSSLPLENQNLAPPDVVP

Parental  CAEEKPF-MMQQPSAQAVVSAVSASLPQSSS-PASPEPRPPHGQ
          C...KPF..MQQPS.QAVV..V.AS.P.SSS.P.SPEP.P....
Retrocopy CTKKKPF>LMQQPSTQAVVFVVLASIP*SSS>PTSPEPQPSQSE

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	13.27 RPM
ERP005899_muscle	0.05 RPM	9.87 RPM
SRP017611_brain	0.00 RPM	13.38 RPM
SRP017611_kidney	0.00 RPM	18.97 RPM
SRP017611_liver	0.00 RPM	4.23 RPM
SRP030211_testis	0.01 RPM	32.39 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1752 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1752 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1752 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023847	1 retrocopy	retro_btau_1752 ,
Cavia porcellus	ENSCPOG00000021914	1 retrocopy	retro_cpor_3,
Mus musculus	ENSMUSG00000040167	1 retrocopy	retro_mmus_2247,
Oryctolagus cuniculus	ENSOCUG00000013340	1 retrocopy	retro_ocun_935,