RetrogeneDB ID: retro_etel_1137

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_217022:11355..11958(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000004543
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNI
• Ensembl ID: ENSETEG00000000952
• Aliases: None
• Description: cyclin I [Source:HGNC Symbol;Acc:1595]

Sequence

>retro_etel_1137
ATGAAGTTTCCAGGACCTTTGGAAAACCAGAGATTGTCTTTCGTATTGGAAAAGGCAATCTCGAGGGAAGCCCAGATGTG
GAAAGTGAATGTCCCCCAAATGCCTACAAGTCAGAATGTGTCTCCATCCCAGAGAGATGAAGTGATCCAGTGGCTGGTCA
AGCTCAAGTACCAGTTCAACCTCTATCCAGAAACATTTGCTCTGGCTAGCAGTCTATTGGACAGGTTTTTAGCAACCATA
AAGGCCCACCCAAAATATTTGAGCTGTATTGCAATCAGCTGTTTTTTCTTAGCTGCCAAGACTGTTGAGGAAGATGAGAG
AATTCCAGTTCTGAAAGTTTTGGCAAGAGACAGTTTCTGTGGATGCTCTTCGACTGAAATTCTGAGAATGGAGAGAATTA
TTCTGGATAAATTGAATTGGGATCTTCACACAGCCACACCATTGGATTTTCTCCACATTGCAGTGTCAACAAGGCCTCAG
TTACTCTTCAGTTTTCCCAAACTGAGCCCATCTCAACATTTGGCATTCCTTACCAAGCAACTCCTCCACTGTATGGCCTG
CAACCAACTTCTGCAATTCAAAGGGTCCATGCTTGCTCCCGGC

Alignment

ORF - retro_etel_1137 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.27 %
• Parental protein coverage: 54.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFPGPLENQRLSFLLEKAISREAQXXXXXXXXXXXXXNVSPSQRDEVIQWLAKLKYQFNLYPETFALAS
          MKFPGPLENQRLSF.LEKAISREAQ.............NVSPSQRDEVIQWL.KLKYQFNLYPETFALAS
Retrocopy MKFPGPLENQRLSFVLEKAISREAQMWKVNVPQMPTSQNVSPSQRDEVIQWLVKLKYQFNLYPETFALAS

Parental  SLLDRFLATVKAHPKYLSCIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSSSEILRMERIILDKLNW
          SLLDRFLAT.KAHPKYLSCIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSS.EILRMERIILDKLNW
Retrocopy SLLDRFLATIKAHPKYLSCIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSSTEILRMERIILDKLNW

Parental  DLHTATPLDFLHIFHAIAVSTRPQLLFSFPKLSPSQHLAFLTKQLLHCMACNQLLQFKGSMLALG
          DLHTATPLDFLHI....AVSTRPQLLFSFPKLSPSQHLAFLTKQLLHCMACNQLLQFKGSMLA.G
Retrocopy DLHTATPLDFLHI----AVSTRPQLLFSFPKLSPSQHLAFLTKQLLHCMACNQLLQFKGSMLAPG

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_1137 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014768	1 retrocopy	retro_cjac_1311,
Echinops telfairi	ENSETEG00000000952	1 retrocopy	retro_etel_1137 ,
Loxodonta africana	ENSLAFG00000029218	1 retrocopy	retro_lafr_295,
Macaca mulatta	ENSMMUG00000019904	1 retrocopy	retro_mmul_2529,
Mus musculus	ENSMUSG00000063015	2 retrocopies	retro_mmus_1211, retro_mmus_2730,
Tarsius syrichta	ENSTSYG00000009907	1 retrocopy	retro_tsyr_834,
Vicugna pacos	ENSVPAG00000011865	1 retrocopy	retro_vpac_197,