RetrogeneDB ID: retro_etel_655

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_132904:266..500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRNP27
• Ensembl ID: ENSETEG00000017344
• Aliases: None
• Description: small nuclear ribonucleoprotein 27kDa (U4/U6.U5) [Source:HGNC Symbol;Acc:30240]

Sequence

>retro_etel_655
AAGAAAGAAGAGATGAGGACAAGAAAGAAAGAAGGTCAGATTCCTGAGGAGGACTCAGAAGGCAAAACAGAGGAAGAGAT
AGAAATGATTGAAGCTATTGGGGTTTGCCTCCACAAAAGGAAGAAGTCAACGGCCATGTAAAATCCTTACGCCATCAATG
TGTTCTCAGAAGAGAAATACAGGCAGGACGTGAATCAAAAAGGTGCATTCAACAGACCTTTGGACTTCATTGCA

Alignment

ORF - retro_etel_655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.65 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKETKEAKNKERQITEEDLEGKTEEEIEM-MKLMGFASFDSTKG-KKVDGSVNAYAINVSQKRKYRQYMN
          .KE......KE.QI.EED.EGKTEEEIEM..KL.GFA...STKG.KK.....N.YAINV....KYRQ..N
Retrocopy KKEEMRTRKKEGQIPEEDSEGKTEEEIEM>LKLLGFA---STKG<KKSTAM*NPYAINVFSEEKYRQDVN

Parental  RKGGFNRPLDFIA
          .KG.FNRPLDFIA
Retrocopy QKGAFNRPLDFIA

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_655 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000037746	4 retrocopies	retro_btau_1352, retro_btau_375, retro_btau_514, retro_btau_515,
Choloepus hoffmanni	ENSCHOG00000003042	1 retrocopy	retro_chof_2589,
Echinops telfairi	ENSETEG00000017344	1 retrocopy	retro_etel_655 ,
Homo sapiens	ENSG00000124380	1 retrocopy	retro_hsap_3387,
Mus musculus	ENSMUSG00000001158	2 retrocopies	retro_mmus_1977, retro_mmus_2105,
Oryctolagus cuniculus	ENSOCUG00000022967	1 retrocopy	retro_ocun_1281,
Pongo abelii	ENSPPYG00000012332	2 retrocopies	retro_pabe_1990, retro_pabe_2782,
Pan troglodytes	ENSPTRG00000012022	1 retrocopy	retro_ptro_2300,
Sus scrofa	ENSSSCG00000025674	1 retrocopy	retro_sscr_285,