RetrogeneDB ID: retro_etel_1562

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_279066:41537..41889(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAP
• Ensembl ID: ENSETEG00000004652
• Aliases: None
• Description: GABA(A) receptor-associated protein [Source:HGNC Symbol;Acc:4067]

Sequence

>retro_etel_1562
ATGAATTTCTTGTATAAAGAGAAGCATCAGTTCGAGAAGCACCGCGCTGAGGGCAAGTAGATCTGAAAAAAAATATCCGG
ACCGGGTCCCGGTGATAGCAGAAAAGGCGCCCAAAGCTCGGATAGGTGATCTGGACAAAAAGAAATACCTGGTACCATCT
GCTCTCACAGTTGGACAACTCTACTTCTTGATCCGGAAGCGAATTCATCTCTGAGCTGAAGATGCCTTATTTTTCTTTGT
CGACAATGTCATTCCGCCCACCAGTGCCACAATGGGTCAGCTATACCAGGAACACCATGAAGAAGACTTCTTTCTATACA
GTGCCTACAGTGACGAGAGTGTCTATGGTCTG

Alignment

ORF - retro_etel_1562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKK-YPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIH
          M.F.YKE.H.FEK.R.EG..I....YPDRVPVI.EKAPKARIGDLDKKKYLVPS.LTVGQ.YFLIRKRIH
Retrocopy MNFLYKEKHQFEKHRAEGK*IXXX>YPDRVPVIAEKAPKARIGDLDKKKYLVPSALTVGQLYFLIRKRIH

Parental  LRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYISYSDESVYGV
          L.AEDALFFFV.NVIPPTSATMGQLYQEHHEEDFFLY..YSDESVYG.
Retrocopy L*AEDALFFFVDNVIPPTSATMGQLYQEHHEEDFFLYSAYSDESVYGL

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_1562 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Echinops telfairi	ENSETEG00000004652	7 retrocopies	retro_etel_1020, retro_etel_1078, retro_etel_1562 , retro_etel_2068, retro_etel_493, retro_etel_666, retro_etel_976,
Echinops telfairi	ENSETEG00000012407	1 retrocopy	retro_etel_1766,
Echinops telfairi	ENSETEG00000015189	2 retrocopies	retro_etel_1050, retro_etel_3,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Mustela putorius furo	ENSMPUG00000010473	2 retrocopies	retro_mputfur_1290, retro_mputfur_258,
Otolemur garnettii	ENSOGAG00000004388	2 retrocopies	retro_ogar_1212, retro_ogar_1224,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,