RetrogeneDB ID: retro_sara_583

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_235859:34912..35500(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNC
• Ensembl ID: ENSSARG00000004726
• Aliases: None
• Description: cyclin C [Source:HGNC Symbol;Acc:1581]

Sequence

>retro_sara_583
CACCGGCTGGTGCCTTTCTGTCAGGGCAAGCTGCGTTCCCGGGCAGGAAACTTTTGACAGAACTCCCACTATTTACAGTG
GATTTGGGATAAACAAGATCTGTTGGAGGAACACCAAAAGGACTTAAAATTTCTCTCAGAAATATATTGGAAATTACAAA
TATTTTTTACAAATGCTATCCAGGCATTAGGTGAACATCTTAAATTAAGACGGCAAGTTATTGCCACTGCTGCAGTCTAT
TTCAAGAGATTCTATGCCAGGTACTCTCAGAAAAGTATAGATCCTGTATTAATGGTCCCTACACGTGTGTTTTTAGCATC
GAAAGTTGAAGAATTTGGAGTAGTCTCAAATACAAGATTGACTGCTGCTGCTACTTCTGTATTAAAGACTAGATTTTCTT
ATGCCTTTCCAAAGGAATTTCCTTAGGGGATGAACCATATACTAGAATGTGAATTCTATCTTTTAGAACTAATGGATTGT
AGCTTGATAGTGTATCATTCTCATAGACCTTTGCTCCAGTATGTGCAGAACATGGGCCAAGAGGACATGTTGCTTCCCCT
TGCATGGAGGATAGTGAATGACACCTAC

Alignment

ORF - retro_sara_583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.8 %
• Parental protein coverage: 65.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HRLVLFYQGKLCSMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNXXXXLGEHLKL
          HRLV.F.QGKL.S.AGNF.Q.SHYLQWI.DKQDLL.E.QKDLKFLSE..YWKLQIFFTN....LGEHLKL
Retrocopy HRLVPFCQGKLRSRAGNF*QNSHYLQWIWDKQDLLEEHQKDLKFLSEI-YWKLQIFFTNAIQALGEHLKL

Parental  RQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLTAAATSVLKTRFSYAFPKE
          R.QVIATA.VYFKRFYARYS.KSIDPVLM.PT.VFLASKVEEFGVVSNTRLTAAATSVLKTRFSYAFPKE
Retrocopy RRQVIATAAVYFKRFYARYSQKSIDPVLMVPTRVFLASKVEEFGVVSNTRLTAAATSVLKTRFSYAFPKE

Parental  FPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTY
          FP..MNHILECEFYLLELMDC.LIVYH..RPLLQYVQ.MGQEDMLLPLAWRIVNDTY
Retrocopy FP*GMNHILECEFYLLELMDCSLIVYHSHRPLLQYVQNMGQEDMLLPLAWRIVNDTY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_583 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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 ,