RetrogeneDB ID: retro_etel_1687

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_287676:4913..5279(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB1A
• Ensembl ID: ENSETEG00000002205
• Aliases: None
• Description: RAB1A, member RAS oncogene family [Source:HGNC Symbol;Acc:9758]

Sequence

>retro_etel_1687
AAGATTCTCATCAATGGCGACAGTGTGGTGGGCAAGCCCAACCTACTATTGAGGTTCACAGATGATACTTTTGATCTAGA
ACTTGCAGCAACAATAGGTGTTGACTTTAAGGTGAAAACAATTTCAGTGGATGGAAATAAAACCAAACTTGCAATTTGGG
ATACTACTGGTCAAGAAAGATTCAGCACATGAACTCCCAGATATTATAGAGGTACACAGGGTGTTATATTAGTGAATGAT
GTTACAAGAAGAGGCACCTTTGTTGAACTGGCTAATTGGTTAAATGAATTGGAAACATACTGCACGAGAAATGACATAGT
CAACATGCTTGTTGGAAATAAAATTGATAAGGAGAAGCGTGAAGTT

Alignment

ORF - retro_etel_1687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.64 %
• Parental protein coverage: 59.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYR
          K.L..GDS.VGK..LLLRF.DDT.......TIGVDFK..TI..DG...KL.IWDT.GQERF.T.T..YYR
Retrocopy KILINGDSVVGKPNLLLRFTDDTFDLELAATIGVDFKVKTISVDGNKTKLAIWDTTGQERFST*TPRYYR

Parental  GAHGIIVVYDVTDQESFNNVKQWLQEIDRYASEN-VNKLLVGNKCDLTTKKV
          G..G.I.V.DVT....F.....WL.E...Y...N.....LVGNK.D.....V
Retrocopy GTQGVILVNDVTRRGTFVELANWLNELETYCTRNDIVNMLVGNKIDKEKREV

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_1687 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002205	2 retrocopies	retro_etel_1687 , retro_etel_413,
Echinops telfairi	ENSETEG00000010795	1 retrocopy	retro_etel_661,
Homo sapiens	ENSG00000138069	2 retrocopies	retro_hsap_2362, retro_hsap_3626,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951,
Oryctolagus cuniculus	ENSOCUG00000017003	1 retrocopy	retro_ocun_800,
Pongo abelii	ENSPPYG00000012360	1 retrocopy	retro_pabe_2135,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727,
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110,
Ictidomys tridecemlineatus	ENSSTOG00000020693	1 retrocopy	retro_itri_1541,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,