RetrogeneDB ID: retro_btau_1584

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:71798996..71800188(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB2
• Ensembl ID: ENSBTAG00000005269
• Aliases: None
• Description: G2/mitotic-specific cyclin-B2 [Source:UniProtKB/Swiss-Prot;Acc:O77689]

Sequence

>retro_btau_1584
ATGGTGCTGTTCCAACGCCCGACAGCATCCACCGATTTAGAGAATAATGACACAGGAGTTAATTCTAAACCTAAAAGTCA
TGTGACTATCAGGTGGGAAGTTTTAGAAGAAATTGGAAATTGGGTTACAACCCGAGCCACACAAGCAGCTCAGAAAATCC
AGAACACTAAAGCACTTTTTCCACCCACCAAAACAACAAATGTCAACAAGCACCTGAAACCTACTGCTTCTGTGAAACCA
GTGCAGATGGAAGTGTTGGCTCCAAAGGGTCCTTCTCCCACACCTCAGGACGTCTCCATGAAGGAAGAGAACCTCTGCCA
AGCTTTCTCTGATGCCTTGCTCTACAAAATTGAGGATATTGATATTGAAGACTGGGAGAACTCTCAGCTCTGCAGTGACT
ACGTGAAGGATATCTACCAGTATCTAAGGCAGCTTGAGGTGCTACAGTCCATAAACCCACATTTCTTAGATGGGAGAGAT
ATAAATGGCTGCATGTGTGCCATCCTGGTGGACTGGCTGGTGCCAGTGCACTCCAAGTTCAGTCTGCTGCAGGAAACGCT
GTACATGTGTGTTGCCATCATGGGCCGATATTTACAGGCTCAGCCAGTCTCTCCGAAGAAGCTTCCGCTGGTTGGCATTA
TGGCACTGCTCTTGGCTTCCAAGTATGAGGAAATGTTTTCTCCAAACATTGAAGGCTTTGTTTACATCACCAACAATGCT
TACACCAGTTCTCAAATTTGAGAAATGTACACTCTGATTTTGAAAGAATTGAAATTTGAGCTGAGTCAACCGTTGCCGCT
ACATTTCTAAGGCAGGCATCGAAAGCCGGGAATATGGATGTTGAATAGCACACTTCAGCCAAATACTTGATGGAGCTGAC
TCTCGTTGACTATGACATGGTGCACTATCACCATTTTAAGGTGGCGGCAGGCACTTCCTGCCTGTCCCAGAAGGTTCTAA
CCAAGAAAAATGGAACTTAAAGCAGCAGTATTACACTGGCTATATAGAGAGAGAGGTGCTGAAGGTCATGCGGCACAAGG
CCAAAAACATTGGGCGCGTCAACAAGAACATGACCAAGCTCACCACCATCAAGAATAAGTATGCAAGTGGCAAACTCCTG
AAGATCAGCACAATTCCTCAGCTGAACTCAAAAGCCATCCAGGAGCTTGCCTCACCTCTGTTGGGACAGTCC

Alignment

ORF - retro_btau_1584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALLRRPTVSTDLENNDTGVNSKPKSHVTIRRAVLEEIGNRVTTRAIQVAKKAQNTKVPVPPTKTTNVSK
          M.L..RPT.STDLENNDTGVNSKPKSHVTIR..VLEEIGN.VTTRA.Q.A.K.QNTK...PPTKTTNV.K
Retrocopy MVLFQRPTASTDLENNDTGVNSKPKSHVTIRWEVLEEIGNWVTTRATQAAQKIQNTKALFPPTKTTNVNK

Parental  HPKPTASVKPVQMDVLAPKGPSPTPQDISMKEENLCQAFSDALLCKIEDIDTEDWENPQLCSDYVKDIYQ
          H.KPTASVKPVQM.VLAPKGPSPTPQD.SMKEENLCQAFSDALL.KIEDID.EDWEN.QLCSDYVKDIYQ
Retrocopy HLKPTASVKPVQMEVLAPKGPSPTPQDVSMKEENLCQAFSDALLYKIEDIDIEDWENSQLCSDYVKDIYQ

Parental  YLRQLEVLQSINPHFLDGRDINGRMRAILVDWLVQVHSKFRLLQETLYMCVAVMDRYLQVQPVSRKKLQL
          YLRQLEVLQSINPHFLDGRDING.M.AILVDWLV.VHSKF.LLQETLYMCVA.M.RYLQ.QPVS.KKL.L
Retrocopy YLRQLEVLQSINPHFLDGRDINGCMCAILVDWLVPVHSKFSLLQETLYMCVAIMGRYLQAQPVSPKKLPL

Parental  VGITALLLASKYEEMFSPNIEDFVYITDNAYTSSQIREMETLILKELKFELGRPLPLH-FLRRASKAGEV
          VGI.ALLLASKYEEMFSPNIE.FVYIT.NAYTSSQI.EM.TLILKELKFEL..PLPLH.FLR.ASKAG..
Retrocopy VGIMALLLASKYEEMFSPNIEGFVYITNNAYTSSQI*EMYTLILKELKFELSQPLPLH<FLRQASKAGNM

Parental  DVEQHTLAKYLMELTLVDYDMVHYHPSKVAAAASCLSQKVL-GQGKWNLKQQYYTGYTESEVLEVMRHMA
          DVE.HT.AKYLMELTLVDYDMVHYH..KVAA..SCLSQKVL..Q.KWNLKQQYYTGY.E.EVL.VMRH.A
Retrocopy DVE*HTSAKYLMELTLVDYDMVHYHHFKVAAGTSCLSQKVL<NQEKWNLKQQYYTGYIEREVLKVMRHKA

Parental  KNVVRVSENMTKFTAIKNKYASSKLLKISTIPQLNSKAIQELASPLLGRS
          KN..RV..NMTK.T.IKNKYAS.KLLKISTIPQLNSKAIQELASPLLG.S
Retrocopy KNIGRVNKNMTKLTTIKNKYASGKLLKISTIPQLNSKAIQELASPLLGQS

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	0.22 RPM
ERP005899_muscle	0.00 RPM	11.46 RPM
SRP017611_brain	0.00 RPM	0.41 RPM
SRP017611_kidney	0.00 RPM	0.18 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.48 RPM	91.09 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1584 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1584 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1584 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004943	1 retrocopy	retro_btau_1335,
Bos taurus	ENSBTAG00000005269	1 retrocopy	retro_btau_1584 ,
Bos taurus	ENSBTAG00000014239	2 retrocopies	retro_btau_1317, retro_btau_600,
Homo sapiens	ENSG00000157456	1 retrocopy	retro_hsap_3816,
Nomascus leucogenys	ENSNLEG00000011543	1 retrocopy	retro_nleu_212,
Otolemur garnettii	ENSOGAG00000012885	2 retrocopies	retro_ogar_1770, retro_ogar_2766,
Pongo abelii	ENSPPYG00000006517	2 retrocopies	retro_pabe_3073, retro_pabe_3074,
Pan troglodytes	ENSPTRG00000007123	1 retrocopy	retro_ptro_2597,
Ictidomys tridecemlineatus	ENSSTOG00000001275	1 retrocopy	retro_itri_229,
Tarsius syrichta	ENSTSYG00000013818	1 retrocopy	retro_tsyr_1402,