RetrogeneDB ID: retro_etel_1568

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_279370:3928..4375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL2
• Ensembl ID: ENSETEG00000000666
• Aliases: None
• Description: phosducin-like 2 [Source:HGNC Symbol;Acc:29524]

Sequence

>retro_etel_1568
CAGCAAAGACTGGCTGAGTGGAAAGCAACTAAACTGAAGAATCAATGTGGAGACGTTTTGGAGATCTCGGGAAAGGATTA
TGTTCAGGAAGTTACCAAAGCTGGTGAGGGCCTATGGGTAATCTTGCACCTTTACAAACAAGGGATTCCCCTCTGTGCTC
TGATAAATCAACACTTCCGTGGACTTGCAAGGAAGTTTCCAGACGCTAAATTTATCAAAGCCATTTCAACAACCTGCATA
CCCAATTATCCTGATAGGAATCTGCCCACGATATTTGTTTATCTCAAAGGAGATATCAAGGCTCAATTTATTGGACCTCT
GGTGTTTGGTGGCATGAACCTGACAAGAGATGAGTTGGAGTGGAAATTGGCCGAGTCTGGAGCAATCAAGACAGACCTGG
AGGAGAACCCCAAGAAACAAGTAGATGTGCTCCTGTCTTCAGTGCGC

Alignment

ORF - retro_etel_1568 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58. %
• Parental protein coverage: 85.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKRLQEWKALKKQN-FGELRE-NINQYVKEVTNAEEDVWVIIHLYRSSIPMCLLVNQHLNLLARKFPETK
          ..RL.EWKA.K..N..G...E.....YV.EVT.A.E..WVI.HLY...IP.C.L.NQH...LARKFP..K
Retrocopy QQRLAEWKATKLKNQCGDVLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCALINQHFRGLARKFPDAK

Parental  FVKAIVNSCIQHYHDNCLPTIFVYKNGQIEGKFIGIMECGGINLKLEELEWKLAEVGAIQTDLEENPKKG
          F.KAI...CI..Y.D..LPTIFVY..G.I...FIG....GG.NL...ELEWKLAE.GAI.TDLEENPKK.
Retrocopy FIKAISTTCIPNYPDRNLPTIFVYLKGDIKAQFIGPLVFGGMNLTRDELEWKLAESGAIKTDLEENPKKQ

Parental  IVDVMVSSIR
          .VDV..SS.R
Retrocopy -VDVLLSSVR

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_1568 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 5 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012692	3 retrocopies	retro_chof_1554, retro_chof_562, retro_chof_737,
Echinops telfairi	ENSETEG00000000666	1 retrocopy	retro_etel_1568 ,
Gorilla gorilla	ENSGGOG00000007908	1 retrocopy	retro_ggor_2890,
Monodelphis domestica	ENSMODG00000020680	2 retrocopies	retro_mdom_1048, retro_mdom_993,
Pan troglodytes	ENSPTRG00000016073	7 retrocopies	retro_ptro_148, retro_ptro_1810, retro_ptro_1865, retro_ptro_2402, retro_ptro_2690, retro_ptro_2784, retro_ptro_675,