RetrogeneDB ID: retro_etel_1803

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_298980:4792..5420(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000002518
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000014092
• Aliases: None
• Description: None

Sequence

>retro_etel_1803
AAGAACAAGTGGGATGTCTATTACTGCCTGGTCAAGGAGAATAGCTGATGGGTTCTCACAGTGCTTTTAAGCAACAACAA
CTCAGAAGAATTCCAACTCTTTGAATGGGTGGTGTGGGCTGTGGACCTGTGTACAGCCCCCTGAAGCTGGAGCCAAGTTC
TGAGGGAGAAAAATGAAGGTGGACATTTGGTGGCTGTGGACCTGCAGGCTCTGGCTGCACTTCCAGGTGTGTTACAGATG
CAAGGGGACATCACTCATCTGCCTACTGCCAAGGAGATCATTCAGCACTTTGAGGACTGCACTGCAGACCTGGTGGTGTG
TGATGGAGTTCCCGATGTAACTGGTCTCCATTATGTGAATGAGTACATGCAGATCCAGATCTTTCCAGCTGCTCTGCACA
TTGCTATGGATGTTTTTAAACCAGGGGGCTGTTTTTTGGCTAAGCTATCCTTAGACTGTGATTTGACACTTCTCTACAGC
CCCCCGAATGTCTTCTCTAATGTGGTGTGTGCCAAGTCCAATGACAACCTCAACTCCAGGATTGAGACCTTCACTGGGAT
GTCAGGGTTCCAACCCTCCTGAGGGCTTCACATCAGACCTGACCAAACCTCTGCTGGGCCACACTTAT

Alignment

ORF - retro_etel_1803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.9 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDKQDVYYRLVQENGWHAHSAFKLLQLNEKFQLFEGVVQLVDLCAAPGS-NQVLSQKIVGGHVVAVDLQA
          ..K.DVYY.LV.EN..............E.FQLFE.VV..VDLC.AP.S..QVL..K..GGH.VAVDLQA
Retrocopy KNKWDVYYCLVKENS*WVLTVLLSNNNSEEFQLFEWVVWAVDLCTAP*SWSQVLREKNEGGHLVAVDLQA

Parental  VAPLPGMLQIQEDITQLSTAKEIIQQFED-PADLVVC----DVTGLHNVDGYLQAQLLPAALNIATQVLK
          .A.LPG.LQ.Q.DIT.L.TAKEIIQ.FED..ADLVVC....DVTGLH.V..Y.Q.Q..PAAL.IA..V.K
Retrocopy LAALPGVLQMQGDITHLPTAKEIIQHFEDCTADLVVCDGVPDVTGLHYVNEYMQIQIFPAALHIAMDVFK

Parental  AGGCFVAKIFRDCDVTLLYSQLWVFSNVVCAKPKSSGNSSIEVFT-VCQGYDPPEGFIPDLTKPLLYHTY
          .GGCF.AK...DCD.TLLYS...VFSNVVCAK.....NS.IE.FT..CQG..PPEGF..DLTKPLL.HTY
Retrocopy PGGCFLAKLSLDCDLTLLYSPPNVFSNVVCAKSNDNLNSRIETFT>GCQGSNPPEGFTSDLTKPLLGHTY

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_1803 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031829	1 retrocopy	retro_btau_27,
Canis familiaris	ENSCAFG00000015339	1 retrocopy	retro_cfam_544,
Erinaceus europaeus	ENSEEUG00000001469	1 retrocopy	retro_eeur_222,
Echinops telfairi	ENSETEG00000014092	3 retrocopies	retro_etel_1697, retro_etel_1803 , retro_etel_1928,
Myotis lucifugus	ENSMLUG00000003977	1 retrocopy	retro_mluc_1329,
Oryctolagus cuniculus	ENSOCUG00000008009	1 retrocopy	retro_ocun_870,
Otolemur garnettii	ENSOGAG00000016174	1 retrocopy	retro_ogar_180,
Sorex araneus	ENSSARG00000007091	1 retrocopy	retro_sara_26,