RetrogeneDB ID: retro_etel_1928

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_315425:2616..3258(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000005852
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_etel_1928
GGGCGGACATCAAAGGACAAGCAGGATGCCGATTGCCGCCTGGCCCCGGAGAACGGCTGGCGCGCCCGCAGCGCTTTTAA
GCTCCTCCAACTCGACGAGGAATTCCAGCTCTTACAAGGGGTGGTGCGGGCTGTGGACCTGTGCGCAGCCCCTGGCAGCT
GGAGCCAAGTCCTGAGCCAGAGGATGACGGACGGACACGTGGTGGCGGTGGACCTGCAGGCGATGGCCCCGCTTCCAGGT
GTGTTCCAGATCCAGGGCGACATCACCCAGCTGTCTACGGCCAAGGAGATCAGTCAGCACTTTGAGGGCTGCCCCGCCGA
CCTCGTCGTGTGTGATGGGGCCCCCGACATAACTGGCCTTCGCGATGTGGATGAGTACATGCAGGCCCAGCTCCTCCTAG
CTGCTCTGAACATTGCTACCCACGTTCTGAAGCCGGGGGGCTGCTTTGTGTCCAAGATCTTCCGAGGCCGGGATGTGACG
CTGCTCTACAGCCAGCTGCGCGTCTTCTTCTCGAAGGTGGTGTGTGCCAAGCCCCGGAGCAGCCGGAACTCCAGCATTGA
GGCCTTCGTTGTCTGCCAGGGCTATGACCCTCCTGCGGGCTTCATACCAGACCTGACCAAACCCTTATTGGACCACACAT
AC

Alignment

ORF - retro_etel_1928 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.23 %
• Parental protein coverage: 64.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GWTSEDKQDVYYRLVQENGWHAHSAFKLLQLNEKFQLFEGVVQLVDLCAAPGS-NQVLSQKIVGGHVVAV
          G.TS.DKQD...RL..ENGW.A.SAFKLLQL.E.FQL..GVV..VDLCAAPGS..QVLSQ....GHVVAV
Retrocopy GRTSKDKQDADCRLAPENGWRARSAFKLLQLDEEFQLLQGVVRAVDLCAAPGSWSQVLSQRMTDGHVVAV

Parental  DLQAVAPLPGMLQIQEDITQLSTAKEIIQQFED-PADLVVC----DVTGLHNVDGYLQAQLLPAALNIAT
          DLQA.APLPG..QIQ.DITQLSTAKEI.Q.FE..PADLVVC....D.TGL..VD.Y.QAQLL.AALNIAT
Retrocopy DLQAMAPLPGVFQIQGDITQLSTAKEISQHFEGCPADLVVCDGAPDITGLRDVDEYMQAQLLLAALNIAT

Parental  QVLKAGGCFVAKIFRDCDVTLLYSQLWV-FSNVVCAKPKSSGNSSIEVFTVCQGYDPPEGFIPDLTKPLL
          .VLK.GGCFV.KIFR..DVTLLYSQL.V.FS.VVCAKP.SS.NSSIE.F.VCQGYDPP.GFIPDLTKPLL
Retrocopy HVLKPGGCFVSKIFRGRDVTLLYSQLRVFFSKVVCAKPRSSRNSSIEAFVVCQGYDPPAGFIPDLTKPLL

Parental  YHTY
          .HTY
Retrocopy DHTY

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_1928 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,