RetrogeneDB ID: retro_btau_1536

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:43580556..43581048(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000001901
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNC
• Ensembl ID: ENSBTAG00000015744
• Aliases: None
• Description: Cyclin-C [Source:UniProtKB/Swiss-Prot;Acc:Q3ZCK5]

Sequence

>retro_btau_1536
AAAGTAGATTTTCATATGCCAAAGGAATTTCCTTATAAGATGAACCATGTATTAGAATGTGAATTCTATCTTTTAGAATT
AATGGATTGTTGCTTAATCTATCATCCTTATAGACCTTTGCTCCAGTATGTGCAGGACATGGGCCAAGAAGACGTGTTGC
TTCCCCATGCATGGAGGATAGTGAATGATACTTACAGAATGGATCTTTGCCTACTATATCCTCCTTTCATGATAGCTTTA
GCTTGCCTGCATGTAGCCTGTGTTGTACAGCAGAAAGATGCCAGAGAGTGGTTTGGTGAGCTTTCTGTGGATATGGAGAA
GATTTTAGAAATAATCAGGGTTATTTTAAAGTTGTATGAGCAGTGGAAAAAATTTGATGAGAGAAAAGAGATGGCAACTA
TTCTTAGTAAGATGCTGAAACCAAAACCACCTCCAAACAGTGAAGGAGAGCAGGGTCCAGATGGAAGTCAGAACTCTAGC
TACAGCCAATCT

Alignment

ORF - retro_btau_1536 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 58.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFSYAFPKEFPYKMNHVLECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDL
          ......PKEFPYKMNHVLECEFYLLELMDCCLI.YHPYRPLLQYVQDMGQED.LLP.AWRIVNDTYR.DL
Retrocopy KVDFHMPKEFPYKMNHVLECEFYLLELMDCCLI-YHPYRPLLQYVQDMGQEDVLLPHAWRIVNDTYRMDL

Parental  CLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDERKEMATILSKMP
          CLLYPPFMIALACLHVACVVQQKDAR.WF.ELSVDMEKILEIIRVILKLYEQWK.FDERKEMATILSKM.
Retrocopy CLLYPPFMIALACLHVACVVQQKDAREWFGELSVDMEKILEIIRVILKLYEQWKKFDERKEMATILSKML

Parental  KPKPPPNSEGEQGPNGSQNSSYSQS
          KPKPPPNSEGEQGP.GSQNSSYSQS
Retrocopy KPKPPPNSEGEQGPDGSQNSSYSQS

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	38.07 RPM
ERP005899_muscle	0.00 RPM	27.34 RPM
SRP017611_brain	0.00 RPM	19.55 RPM
SRP017611_kidney	0.00 RPM	31.06 RPM
SRP017611_liver	0.00 RPM	10.42 RPM
SRP030211_testis	0.02 RPM	21.29 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1536 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1536 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015744	3 retrocopies	retro_btau_1206, retro_btau_1536 , retro_btau_1836,
Callithrix jacchus	ENSCJAG00000001388	1 retrocopy	retro_cjac_780,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216, retro_dnov_2243,
Echinops telfairi	ENSETEG00000002643	1 retrocopy	retro_etel_1441,
Otolemur garnettii	ENSOGAG00000001116	1 retrocopy	retro_ogar_2123,
Sorex araneus	ENSSARG00000004726	2 retrocopies	retro_sara_141, retro_sara_583,