RetrogeneDB ID: retro_etel_1560

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_278901:146653..146860(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSETEG00000012346
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]

Sequence

>retro_etel_1560
ATGGCCTCCCGGAATGGTGACCCAGCTGCAGCCAGCTTCATAGCCACCCGAGAGGGGGTGGAACCCAGCAGGGGGCGTCA
CCTGGGGTTCTGTGGGTAGGAGGCTACCACAGGAGCTGAGGACCCTCATCAGGTCTGGTGACAAAGGTACATCTGCCTTC
CCGGAATCAGACCACCTTTTCAAGTGGGTGGGGGCATCCACGCAGCC

Alignment

ORF - retro_etel_1560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.75 %
• Parental protein coverage: 70.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASQNRDPAAASVVAARKGAEPS-GGAARGSVGKXXXXXXXXXXMSDDKGISAFPESDNLFKWIGT-IHG
          MAS.N.DPAAAS..A.R.G.EPS.GG...GSVG............S.DKG.SAFPESD.LFKW.G..IH.
Retrocopy MASRNGDPAAASFIATREGVEPS>GGVTWGSVGRRLPQELRTLIRSGDKGTSAFPESDHLFKWVGA<IHA

Parental  A
          A
Retrocopy A

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_1560 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 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014102	2 retrocopies	retro_cpor_1007, retro_cpor_211,
Echinops telfairi	ENSETEG00000012346	18 retrocopies	retro_etel_1212, retro_etel_1500, retro_etel_1560 , retro_etel_157, retro_etel_1634, retro_etel_1729, retro_etel_1853, retro_etel_1856, retro_etel_2013, retro_etel_221, retro_etel_321, retro_etel_324, retro_etel_400, retro_etel_628, retro_etel_689, retro_etel_764, retro_etel_824, retro_etel_909,
Loxodonta africana	ENSLAFG00000003164	1 retrocopy	retro_lafr_73,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mustela putorius furo	ENSMPUG00000017619	2 retrocopies	retro_mputfur_103, retro_mputfur_189,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,