RetrogeneDB ID: retro_etel_645

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_125755:316..780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX3
• Ensembl ID: ENSETEG00000003537
• Aliases: None
• Description: sorting nexin 3 [Source:HGNC Symbol;Acc:11174]

Sequence

>retro_etel_645
GCAGAGTCGGTGGAAGATACCTGGGGCTGATCACCAAGCCGCAGAACCTGAATGACGCCTACGGGCCGCCCAGCAACTTC
CTCGAGATCGATGTGAGCAACCCCCAGACCGTGGGGGTCAGCAGGGGCCGCTTCACCACCCACGAAATCAGGGTCAAGAC
AAATCTTCCTCTTTTCAAGCTGAAGGAATCTCCTGTTAGAAGTGACTTTGAATAGCTGTGAAGTGCATTAGAGAGAGCAA
GCAAGACTGTAGTTCCCCCACGCCCTGGAAAAGCCTTTTGACGTCAGCTTCCTTTCAGAGGAGATGGGATCTTGGATGAC
AGTTTTATCTAGGAAGCACGGGCTGCAGCAGTTATAAACAAGGTCGCTGGTCATCCTCCGGCACAGGGTGAGCGTGGTCT
TCACATGTTTTCACAAGACAAAATCATTGATAAGCGCTATACTCCATCCAAAATAAGACATGCC

Alignment

ORF - retro_etel_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.16 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AETVADT-RRLITKPQNLNDAYGPPSNFLEIEVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRR
          AE.V.DT...LITKPQNLNDAYGPPSNFLEI.VSNPQTVGV.RGRFTT.EIRVKTNLP.FKLKES.VR..
Retrocopy AESVEDT<LGLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVSRGRFTTHEIRVKTNLPLFKLKESPVR--

Parental  YSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDSFIEERKHGLEQFINKVAGHPLAQNERC
          .SDFE.L.S.LER.SK.VVPP.PGKAF.RQLPFRG.DGI.DDSFI.E........INKVAGHP.AQ.ER.
Retrocopy -SDFE*L*SALERASKTVVPPRPGKAF*RQLPFRG-DGILDDSFI*EAR--AAAVINKVAGHPPAQGERG

Parental  LHMFLQDEIIDKSYTPSKIRHA
          LHMF.QD.IIDK.YTPSKIRHA
Retrocopy LHMFSQDKIIDKRYTPSKIRHA

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_645 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015256	1 retrocopy	retro_eeur_525,
Echinops telfairi	ENSETEG00000003537	3 retrocopies	retro_etel_1331, retro_etel_645 , retro_etel_924,
Felis catus	ENSFCAG00000024997	1 retrocopy	retro_fcat_1705,
Loxodonta africana	ENSLAFG00000018131	1 retrocopy	retro_lafr_579,
Oryctolagus cuniculus	ENSOCUG00000005858	2 retrocopies	retro_ocun_1022, retro_ocun_750,
Tupaia belangeri	ENSTBEG00000011755	3 retrocopies	retro_tbel_2964, retro_tbel_3503, retro_tbel_3929,
Tursiops truncatus	ENSTTRG00000008868	2 retrocopies	retro_ttru_1028, retro_ttru_1103,