RetrogeneDB ID: retro_etel_1441

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_266305:1665..2122(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNC
• Ensembl ID: ENSETEG00000002643
• Aliases: None
• Description: cyclin C [Source:HGNC Symbol;Acc:1581]

Sequence

>retro_etel_1441
ATGGTCACTCCGCGGCTGCTCTGCCAGCTGGTGCTTCTCTATCAGGGCAAGCTCTGTTCCATGGCAGGAACTTTTGGCAG
AGCTCCCACTATTTGCGATGGATTTTGGGTAAATCAGGCCTTTTGAAGAGTGCCAAAAGGACTTAAATTTTCTCTCAGAA
GAAGAGTACTGGAAATTCCAGATATTTTTTACAAATGCTATCCAGGCATTAGGTGAACGTCTTAAATGAAGACAGCAAGT
CATTGCTACTGCTAGGGTCTATTTCAAGAGATTCTATGCCAGGTACTCTCTGAAAAGGATAGATCCTACATGAATGGCTC
CAACTTGTGTGCTTGGGGCATCCAAAAGAGAGGAGTTTGGAGCAGTCTCAAACACAAGATTGATTTCTGCCATTTCTGTA
TTCAAAACTAGATTTTCATATGCTTTCCCAAAGGAGTTTCCTTATAGGGTGAATCAT

Alignment

ORF - retro_etel_1441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.21 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVAPR----LVLFHQDKLCSMAG-NFWQSSHYLQWILDKQDLLK-ERQKDLKFPSEEEYWKLQIFFTNVI
          MV.PR....LVL..Q.KLCSMAG.NFWQSSHYL.WIL.K..LLK.E.QKDL.F.SEEEYWK.QIFFTN.I
Retrocopy MVTPRLLCQLVLLYQGKLCSMAG<NFWQSSHYLRWILGKSGLLK<ECQKDLNFLSEEEYWKFQIFFTNAI

Parental  QALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKT
          QALGE.LK.RQQVIATA.VYFKRFYARYSLK.IDP..MAPTCV..ASK.EEFG.VSNTRLI..A.SV.KT
Retrocopy QALGERLK*RQQVIATARVYFKRFYARYSLKRIDPT*MAPTCVLGASKREEFGAVSNTRLI-SAISVFKT

Parental  RFSYAFPKEFPYRMNH
          RFSYAFPKEFPYR.NH
Retrocopy RFSYAFPKEFPYRVNH

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1441 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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,