RetrogeneDB ID: retro_btau_1424

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:51171821..51172572(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK2
• Ensembl ID: ENSBTAG00000004021
• Aliases: None
• Description: Cyclin-dependent kinase 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5E9Y0]

Sequence

>retro_btau_1424
GCCGTATGAGAGATCTCTCGGCTTAAGGAGTTTAATCACCCTAATATTGTCAAACTGCTGGATGTCATTCACACAGAAAA
CAAACTCTACCTGGTTTTTGAGTTTCTGCACTAGGATCTCAAGAAATTCATGGATGCCTCTGTGCTCACTGGCATTCCTC
TTCCCCTCATAAAGAGCTACTTGTTCCAGCTGCTCCAGGGCCTCGCTTTCTGCCACTCTCATTGGGTCCTGCACCGAGAC
CTCAAACCTCAGAATCTGCTTATCAACGCAGATGGGTCCATCAAGCTAGCAGACTTCGGACTAGCCAGAGCTTTTGGGGT
CCCTGTTCATACTTATACCGACGAGGTGGTGACTCTGTGGTACTGAGCACTGGAAATCCTTCTGGGCTGCAAATACTACT
CCATAGCTGTGGACATCTGGAGCCTCGGTTGCATCTTTGCTGAGATGGTGACCCACTGGGCCCTATTTCCTGGAGACTCT
GAGATCAACCAACTCTTCCAGATCTTTCTTCCCTGGAGACCCCAGATGAGGTGGTTTGGCCAGGAGTTATTTCTATGTCG
GATTATAAGCCAAGTTTCCCCAAGAGGGCCAGGCAAGATTTTAGCAAAGTGGTGCCACCCCGGATGAAGATGGATGGAGC
TTGTTATTGCAAATGCTGTACTACAAGCCTAACAAGTGGGTTTCAGCCAAGGCAGCTCTGGCTCACCCTTTCTTCCAGGA
TGTGACCAAGCCAGTACCTCACCTTCGACTC

Alignment

ORF - retro_btau_1424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.75 %
• Parental protein coverage: 84.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAF
          A..EIS.LKE.NHPNIVKLLDVIHTENKLYLVFEFLH.DLKKFMDAS.LTGIPLPLIKSYLFQLLQGLAF
Retrocopy AV*EISRLKEFNHPNIVKLLDVIHTENKLYLVFEFLH*DLKKFMDASVLTGIPLPLIKSYLFQLLQGLAF

Parental  CHSHRVLHRDLKPQNLLINADGSIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIW
          CHSH.VLHRDLKPQNLLINADGSIKLADFGLARAFGVPV.TYT.EVVTLWY.A.EILLGCKYYS.AVDIW
Retrocopy CHSHWVLHRDLKPQNLLINADGSIKLADFGLARAFGVPVHTYTDEVVTLWY*ALEILLGCKYYSIAVDIW

Parental  SLGCIFAEMVTRRALFPGDSEIDQLFRIF-RTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPL-
          SLGCIFAEMVT..ALFPGDSEI.QLF.IF...L.TPDEVVWPGV.SM.DYKPSFPK.ARQDFSKVVPP..
Retrocopy SLGCIFAEMVTHWALFPGDSEINQLFQIF<SSLETPDEVVWPGVISMSDYKPSFPKRARQDFSKVVPPR<

Parental  DEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
          DEDG.SLL.QML.Y.PNK..SAKAALAHPFFQDVTKPVPHLRL
Retrocopy DEDGWSLLLQMLYYKPNKWVSAKAALAHPFFQDVTKPVPHLRL

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	4.11 RPM
ERP005899_muscle	0.00 RPM	6.44 RPM
SRP017611_brain	0.09 RPM	1.83 RPM
SRP017611_kidney	0.00 RPM	9.36 RPM
SRP017611_liver	0.00 RPM	4.68 RPM
SRP030211_testis	0.08 RPM	45.28 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1424 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1424 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003168	1 retrocopy	retro_amel_1525,
Bos taurus	ENSBTAG00000004021	1 retrocopy	retro_btau_1424 ,
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Erinaceus europaeus	ENSEEUG00000014081	1 retrocopy	retro_eeur_445,
Pteropus vampyrus	ENSPVAG00000007555	1 retrocopy	retro_pvam_794,
Tupaia belangeri	ENSTBEG00000005123	1 retrocopy	retro_tbel_4151,