RetrogeneDB ID: retro_etel_1537

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_277497:19629..20354(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COIL
• Ensembl ID: ENSETEG00000003687
• Aliases: None
• Description: coilin [Source:HGNC Symbol;Acc:2184]

Sequence

>retro_etel_1537
AAAGGCAAGACAGCCAAACTATAATCTCCCAGCTCAGATTCCAGTTCTAAGTCAGATGACCAGAGCACAGCATCACAGAG
AACCCTGGAGTGTGCTGCAAGCTTCTTAAAGATGGTGGGTCTCTTAGAAGGAAGAGGTCGTCCAGGGCCAGGGTCATCAT
CACAGATGCCAAGTGCTATTGGATGGAACCATTCTGATTCCAATGGTGGTAGACAGGCTCCTGGCCCTCCTCTCAACTTG
TCTCTCCCGGCCAATCTGGGATGAGTTTAAGGTAGAGGAGATGACCTTTCTTGGAAAGAATCCAGGGGTCAGAGCTTGCA
GAAAGAGGATGAGGTCCAGGGCAAACCATTCCCTGTGTTTTAAGTAAAAACAATGATTATCAAAAGCAGCATTTCAGTTA
ACTGAAATGATAACAAACTCATCCACTATTATCCAAAATCCTGTAGAGATAAGCCAGAAGGATTATAGTGTGTTATCACT
GTTAGCAGCTGCCCCCAGGTTGGAGAAAAGATTGCATTTAAACTTTTGGAACTAACATCTGATTACTACCCTGATGTGTC
TGGATTATAAGGAAGGGAACCATTACGTCACAATCCAGAGCCCAATAAGTTGATATATAAATCCTTTCATCTGTAACTGC
CTCGAAAGAACCTGGAAAGCTGGATTTGGCTTATCACAGTGAATATGGAATGGAGGTGGTGGAATATGTTCTGATTCAGA
AGAGG

Alignment

ORF - retro_etel_1537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.71 %
• Parental protein coverage: 52.51 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KGKAAKPSSSSSDSSSESDGPSMPSQKTPECAAGVPQTADLLAGRGGPPGPGSSSQMPSAIRWKHFDANT
          KGK.AK..S.SSDSSS.SD..S..SQ.T.ECAA.......LL.GRG.P.GPGSSSQMPSAI.W.H.D.N.
Retrocopy KGKTAKL*SPSSDSSSKSDDQSTASQRTLECAASFLKMVGLLEGRGRP-GPGSSSQMPSAIGWNHSDSNG

Parental  SRQ--GPPLNLSLPASLGRGWGRGEDLSWKGPRG-RGVRGRGRGRGQPISCVLNRSSDYQKQQQLTEILT
          .RQ..GPPLNLSLPA.LG...GRG.DLSWK..RG.R..R.R.R.R.....C............QLTE..T
Retrocopy GRQAPGPPLNLSLPANLG*V*GRGDDLSWKESRG>RACRKRMRSRANHSLCFK*KQ*LSKAAFQLTEMIT

Parental  NSSTLIQNPAEVSQKDYSVLPLLAAA-PQVGDKIAFKLLELTSDYSPDVS-DYKEG-KILSHNPE-TQQV
          NSST.IQNP.E.SQKDYSVL.LLAAA.PQVG.KIAFKLLELTSDY.PDVS.DYKEG...L.HNPE..Q.V
Retrocopy NSSTIIQNPVEISQKDYSVLSLLAAA<PQVGEKIAFKLLELTSDYYPDVS>DYKEG<EPLRHNPE<AQ*V

Parental  DIEILSSLPALKEPGKFDLVYHNENGTEVVEYAVTQEK
          DI.ILSS..A.KEPGK.DL.YH.E.G.EVVEY...Q..
Retrocopy DI*ILSSVTASKEPGKLDLAYHSEYGMEVVEYVLIQKR

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_1537 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008740	1 retrocopy	retro_chof_1121,
Callithrix jacchus	ENSCJAG00000013960	1 retrocopy	retro_cjac_2240,
Dasypus novemcinctus	ENSDNOG00000023961	1 retrocopy	retro_dnov_1986,
Echinops telfairi	ENSETEG00000003687	1 retrocopy	retro_etel_1537 ,
Nomascus leucogenys	ENSNLEG00000008026	1 retrocopy	retro_nleu_1014,
Oryctolagus cuniculus	ENSOCUG00000011345	1 retrocopy	retro_ocun_1798,
Pongo abelii	ENSPPYG00000008248	1 retrocopy	retro_pabe_305,
Tupaia belangeri	ENSTBEG00000008882	4 retrocopies	retro_tbel_2118, retro_tbel_3549, retro_tbel_3961, retro_tbel_838,