RetrogeneDB ID: retro_etel_1118

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_214879:1330..1549(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEDD8
• Ensembl ID: ENSETEG00000018391
• Aliases: None
• Description: neural precursor cell expressed, developmentally down-regulated 8 [Source:HGNC Symbol;Acc:7732]

Sequence

>retro_etel_1118
ATTACAGTGAAGAAGATGACCCGAAAGGAGTTCGAAATTGACATTGAACCCATGGGTGAGGTGGAGCGAATTAAGGAGAA
AGAGGGATTCCCCCCTCAGCTACGGTGCCTCGTCTACAGAGAAATGAATGACGAGAAGACAGCAGCCTACTACAAGATCT
TAGGTGGCTCAGTCCTCCACCGTGTGTTGGCTCTGAGAGGAGGAGGTGGTCGCTTGGGC

Alignment

ORF - retro_etel_1118 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.62 %
• Parental protein coverage: 96.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLA
          I.VK..T.KE.EIDIEP...VERIK....EKEG.PPQ...L.Y....MNDEKTAA.YKILGGSVLH.VLA
Retrocopy ITVKKMTRKEFEIDIEPMGEVERIK----EKEGFPPQLRCLVY--REMNDEKTAAYYKILGGSVLHRVLA

Parental  LRGGGGRPG
          LRGGGGR.G
Retrocopy LRGGGGRLG

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_1118 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 9 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038842	1 retrocopy	retro_btau_89,
Choloepus hoffmanni	ENSCHOG00000001228	5 retrocopies	retro_chof_1012, retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus	ENSCJAG00000006876	1 retrocopy	retro_cjac_4064,
Erinaceus europaeus	ENSEEUG00000011640	2 retrocopies	retro_eeur_165, retro_eeur_43,
Echinops telfairi	ENSETEG00000018391	2 retrocopies	retro_etel_1118 , retro_etel_1677,
Homo sapiens	ENSG00000129559	1 retrocopy	retro_hsap_180,
Macaca mulatta	ENSMMUG00000029409	1 retrocopy	retro_mmul_2236,
Monodelphis domestica	ENSMODG00000003254	1 retrocopy	retro_mdom_1681,
Vicugna pacos	ENSVPAG00000009104	4 retrocopies	retro_vpac_270, retro_vpac_316, retro_vpac_480, retro_vpac_558,