RetrogeneDB ID: retro_etel_1308

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_244999:6834..7486(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000007634
• Aliases: None
• Description: None

Sequence

>retro_etel_1308
GTTCACCTTGAACAGAATGAGGAGGATATTGGCGTAGAAGACCAGGGTTTGGTGTTTGGCTATGCCACTGATGAAACTGA
AGAATGTATGTCAATATCCATTGTCTTAACACCAAAACTCAATTCCACACTTGCTCAACTATTTCACAATGGTACGTTAC
CTTGGTTATGCTCAGATTCTAAAACTCAAGTGACTGTGCAGTACGCACAGGATCAAGATCCCATAAAAGTCCACACAATT
GTTGTTTCTGTTCAGCATGAGGACGCCGCTTCTCTTGATGAGGTGAGGGGTGCCTAAAGAAAGTCATTAACACAATTGTG
CCTGCAAAGTATCTTGATGAAGATACAATCTACCACCTATATCCAAAATTTGTTACTGGTGACTATCAGGGTGCTGCTGG
TTTGGCTGGCCTGAAGATCACTGTAGCCATTTACAGTGGTTGAGGACCTCATGGAACAGTTGCCTTTTCAGGAAAAGATT
ATACCCATGTGGAACGTTCAGCTGCTTATGCTGCTGTTGGGTGGCAAGTTCCTTTGTGAAAGGAGGTCTGTGCAGAAGCG
ATTTTGTCCAGGTCTCTTACACTACTGGAGTTTTTCACCTATTGTCGATATCCATTTTCCATTATGGCACCTCTCAGAAG
AGTGAGAGAAAG

Alignment

ORF - retro_etel_1308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.47 %
• Parental protein coverage: 56.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VHLDRNEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQ
          VHL..NEEDIG..DQGL.FGYATDETEECM...IVL..KLN..LA.L..NGTLPWL..DSKTQVTVQY.Q
Retrocopy VHLEQNEEDIGVEDQGLVFGYATDETEECMSISIVLTPKLNSTLAQLFHNGTLPWLCSDSKTQVTVQYAQ

Parental  DRGAVLPIRVHTIVISVQHDEDVCLDEMRDA-LKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDA
          D.....PI.VHTIV.SVQH.....LDE.R.A.LK.KVI...VPAKYLDEDTIYHL.P...FV.G..QG.A
Retrocopy DQD---PIKVHTIVVSVQHEDAASLDEVRGA<LK-KVINTIVPAKYLDEDTIYHLYP--KFVTGDYQGAA

Parental  GLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAA-RWVAKSLVKGGLCRRVLVQVSYAIGVAHPL
          GL.G.KI.V..Y.G.G.HG..AFSGKDYT.V.RSAAYAA..WVA.S.VKGGLCR...VQVSY..GV.H.L
Retrocopy GLAGLKITVAIYSG*GPHGTVAFSGKDYTHVERSAAYAA<CWVASSFVKGGLCRSDFVQVSYTTGVFHLL

Parental  SISIFHYGTSQKSERE
          SISIFHYGTSQKSER.
Retrocopy SISIFHYGTSQKSERK

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_1308 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013959	1 retrocopy	retro_chof_30,
Echinops telfairi	ENSETEG00000007634	2 retrocopies	retro_etel_1308 , retro_etel_1532,
Echinops telfairi	ENSETEG00000015680	4 retrocopies	retro_etel_1669, retro_etel_1813, retro_etel_597, retro_etel_977,
Ornithorhynchus anatinus	ENSOANG00000003060	1 retrocopy	retro_oana_84,
Otolemur garnettii	ENSOGAG00000026925	1 retrocopy	retro_ogar_1580,
Rattus norvegicus	ENSRNOG00000013520	2 retrocopies	retro_rnor_2032, retro_rnor_955,