RetrogeneDB ID: retro_etel_1893

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_312121:3927..4192(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSETEG00000014825
• Aliases: None
• Description: ribosomal protein L11 [Source:HGNC Symbol;Acc:10301]

Sequence

>retro_etel_1893
TCCATCCACTGCACAGTCCATGGGGCCAAGGCAGAAGAAATCTTGGAGAAAGGTATAAAGGTTCAGGAGTAGTAGTTACG
AAACACTAACTTTTCTGTTACCAGAAACTTTGGATTTGGGATCCAAGAACACATTTATGTGGGGAGGAACATGACCCTAG
CCTGGGGTCTATGGCTGGGACTTGGATGGGGTGCTGGAGAGGCCAAGCTTCAGCTTTGCAGACAAGAAGCACAACGCAGC
TTGCATCTGGCCCAAACACGGAATC

Alignment

ORF - retro_etel_1893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.64 %
• Parental protein coverage: 85.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDL-GIKYDPSI-GIYGLDFYVVLGR
          ..HCTV.GAKAEEILEKG.KV.E..LR..NFS.T.NFGFGIQEHI...G...DPS..G.YG.D...VL.R
Retrocopy SIHCTVHGAKAEEILEKGIKVQE**LRNTNFSVTRNFGFGIQEHIYV<GEEHDPSL<GVYGWDLDGVLER

Parental  PGFSIADKKRRTGCIGAKHRI
          P.FS.ADKK....CI..KH.I
Retrocopy PSFSFADKKHNAACIWPKHGI

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_1893 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 11 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Dasypus novemcinctus	ENSDNOG00000011230	2 retrocopies	retro_dnov_1453, retro_dnov_605,
Dipodomys ordii	ENSDORG00000012496	1 retrocopy	retro_dord_143,
Echinops telfairi	ENSETEG00000014825	8 retrocopies	retro_etel_1054, retro_etel_136, retro_etel_1452, retro_etel_1893 , retro_etel_2018, retro_etel_500, retro_etel_62, retro_etel_948,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Macropus eugenii	ENSMEUG00000013738	3 retrocopies	retro_meug_488, retro_meug_517, retro_meug_633,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica	ENSMODG00000012828	1 retrocopy	retro_mdom_641,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus	ENSOANG00000000321	1 retrocopy	retro_oana_49,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,