RetrogeneDB ID: retro_btau_1206

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:9371594..9372441(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000015741
• 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_1206
ATGGCAGGGAACTTTTGGCAGAGCTCCACTATTTACAATGGATTTTGGACAAACAAGATCTGTTGAAGGAATGCCAAAAA
GATTTAAAGTTTCTCTTGGAAGAAGAGTATGGGAAATTACAGATATTTTTTACAAATGTTATCCAAGCATTAGGTGAACA
ACTTAAATTAAGACAACAAGTTATTGCCACTGCTACGGTCTATTTCAAGAGATTCTATGCAAGGTATTCTCTGAAAAGTA
TAGATCCTGTATTAATGGGTCCTACATGTGTGTTTTTGGCATCCAAAGTAGAGGAATTTGGAGTAGTATCAAATACAAGA
TTGATTGCTGCTGCTACTTCTGTATTGAAAACTAGATTTTCATATGCCTTTCTAAAGGAATTTCCTTATAAGATGAACCA
TGTATTAGAATGTGAATTCTATCTTTTAGAATTAATGGATTGTTGCTTGATAGTGTATCATCCTTATAGACCTTTGTTCC
AGTATGTGCAGGACATGGGCCAAGAAGACATACTGCTTTCCCTTGCTTGGAGGATAGTAAATGATACCTACAGAACGGAT
CTTTGCCTACTGTATCCTCCTTTCATGATAGCTTTAGCTTGCCTACATGTAGCCTGTGTTGTACAGCAGAATGATGCCAG
ACAGTGGTTTGCTGAGCTTTCTGTGGATATGGAGAAGATTTTGGAAATAATCAGGGTTATTTTAAAGTTGTATGAGCAGT
GGAAAATTTTTGATGAGAGAAAAGAGAGGCAACTATTCTTAGTAAGATGCCGAAACCAAAACCTCCTCCAAACAGTGAAG
GAGAGCAGGGTCCAAATGGAAGTCAGAACTCTAGCTACAGCCAATCT

Alignment

ORF - retro_btau_1206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGNFWQSS-HYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYF
          MAGNFWQSS.HYLQWILDKQDLLKE.QKDLKFL.EEEY.KLQIFFTNVIQALGE.LKLRQQVIATATVYF
Retrocopy MAGNFWQSS<HYLQWILDKQDLLKECQKDLKFLLEEEYGKLQIFFTNVIQALGEQLKLRQQVIATATVYF

Parental  KRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYKMNHVLECE
          KRFYARYSLKSIDPVLM.PTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAF.KEFPYKMNHVLECE
Retrocopy KRFYARYSLKSIDPVLMGPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFLKEFPYKMNHVLECE

Parental  FYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQ
          FYLLELMDCCLIVYHPYRPL.QYVQDMGQED.LL.LAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQ
Retrocopy FYLLELMDCCLIVYHPYRPLFQYVQDMGQEDILLSLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQ

Parental  QKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDERKEM-ATILSKMPKPKPPPNSEGEQGPNGSQNS
          Q.DARQWFAELSVDMEKILEIIRVILKLYEQWK.FDERKE..ATILSKMPKPKPPPNSEGEQGPNGSQNS
Retrocopy QNDARQWFAELSVDMEKILEIIRVILKLYEQWKIFDERKER<ATILSKMPKPKPPPNSEGEQGPNGSQNS

Parental  SYSQS
          SYSQS
Retrocopy SYSQS

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	0.05 RPM	19.55 RPM
SRP017611_kidney	0.00 RPM	31.06 RPM
SRP017611_liver	0.15 RPM	10.42 RPM
SRP030211_testis	0.00 RPM	21.29 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1206 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1206 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1206 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,