RetrogeneDB ID: retro_etel_1532

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_277164:13016..13750(+)
• 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_1532
GGATTTGACTACAAGTCTTGTGCTGTTCTGGTAGCTTTGCAACAACAGCCGCCAGATGTTCTTCAAGGGGTTCACCTTGG
CCAGAATGAGCAGAGAGAAGTGCAGGAGACCAGGGCACAGTGTTTGGTTATGTCACTGATGAATCTGAAGAAGGTTTGCC
TTTAACCATTGTCTTGGCACACAAGCTCAATGACAGACTTGCTGAACTACGTCGCAATGGCACCTTACCTTGGTTACACC
CAGATCCTAAAACTCAGTGACTGTGCAGTACATGCAGGATGGAGGTGCTGTGCTGCCCATCAGAGTCCACACAATTGTTA
TATCAGTTCAGCAGGATGAAGGTGTTTGTCTGTATGAGATGAGGGAGGCCCTGAAGGAGAAAGTCATTAAAGCCATAGTT
CTGCAGAGTATCTTGATGAGGACACAATCTACCACTGACAGCCCACTGGTAGATGGGTTATTGGGGGGCCTCGGGGTGAT
GCTGGTGTGACTGGCCGGAAGATCATTGTGGACACTTATGGAGGCTGGGGAGCTCATGGAGGAGGTGGCTTTTCAGGAAA
GGGTTGTACCAAGGTGGACCGCTTGGCTGCTTATGCTGCCTGTTGGGTGGCTAAATCCCTTGTTACAGGAGGCTGTGCAG
AAAGGTTCTAGGGCAGCTCTCTTATGCTACTGGAGTTTCTCAGCCAGGGTCCGTTGCCATTTTCCATTATGAAACCTCTC
AGAAGAGTGAGAGA

Alignment

ORF - retro_etel_1532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78. %
• Parental protein coverage: 62.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GFDYKTCNVLVALEQQSPDIAQGVHLDRNEE-DIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAE
          GFDYK.C.VLVAL.QQ.PD..QGVHL..NE.....AGDQG..FGY.TDE.EE..PLTIVLAHKLN..LAE
Retrocopy GFDYKSCAVLVALQQQPPDVLQGVHLGQNEQ<ERSAGDQGTVFGYVTDESEEGLPLTIVLAHKLNDRLAE

Parental  LRRNGTLPWLRPDSKTQ-VTVQYMQDRGAVLPIRVHTIVISVQHDEDVCLDEMRDALKEKVIKAVV-PAK
          LRRNGTLPWL.PD.KTQ.VTVQYMQD.GAVLPIRVHTIVISVQ.DE.VCL.EMR.ALKEKVIKA.V..A.
Retrocopy LRRNGTLPWLHPDPKTQ<VTVQYMQDGGAVLPIRVHTIVISVQQDEGVCLYEMREALKEKVIKAIV<SAE

Parental  YLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKS
          YLDEDTIYH.QP.GR.VIGGP.GDAG.TGRKIIVDTYGGWGAHGGG.FSGK..TKVDR.AAYAA.WVAKS
Retrocopy YLDEDTIYH*QPTGRWVIGGPRGDAGVTGRKIIVDTYGGWGAHGGGGFSGKGCTKVDRLAAYAACWVAKS

Parental  LVKGG-LCRRVLVQVSYAIGVAHPLSISIFHYGTSQKSER
          LV.GG.LCR.VL.Q.SYA.GV..P.S..IFHY.TSQKSER
Retrocopy LVTGG<LCRKVLGQLSYATGVSQPGSVAIFHYETSQKSER

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_1532 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,