RetrogeneDB ID: retro_etel_977

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_194819:8875..9769(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000006073
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000015680
• Aliases: None
• Description: None

Sequence

>retro_etel_977
GAGGGCACCTTCCTGTTCACCTCGGAGTCCGTGGGGGAAGGACACCCAGATGAGATTTGTGACCAGATCAGTGATGCTGT
TCTTTATGCCCACCTTCAGTAGGATCCTGACGCCAAAGTGGCTTGTGAAACTGTTATTATTAACACTGGACTTGTTATTC
TTGCTGGGAAAATTACATCCAGAGCTGCCATTGACTACCAGAAAGTAGTTCGTGATACCATCAAGCACATTGGCTATGAT
GATTCTTCCAAAGGATTTGACTACAAGGCTTGTGCTGTTCAGGTGGCTTTGGAACAACAGTCACCAGACATTGCTCAAGG
GGGTCACCTTGACCTGAATGAGAAGGAGGTTGGTGCAGGAGACTACCAGGGCATGGTGTTTGGTTATGCCGCTGATGAAA
CTGAAGAATGTATGCCTTTAACCCTTGTCTTAGCCCACCAGCTCAATGCCAAACTTGCTGAACTACGTCGCAATGGCACC
TTACCTTGGTTACGCCCAGATTCTAAAACTCAAGTGGCTGTGCAGTACATGAAGGATCGAGGTGCTGTGCTGCCCATCAG
AATCCACGAAATTGTTATGTCTGTTCAGCATGATGAAGATGTTTCTCTGGATGAGATGAGGGAGGCCCTGAAGGAGAAAG
TCATTAAAGTCGTTGTTCCTGCAAAGTATCTTGATGAGGACACAATCTACCACATACAGCCTAGTGGCAGATTTGTAATT
GGGGGTCCTCAGGCTAGTACTGGTTTGAGTGGCCAGAAGATAATTTTGGACACTTATGGAGGCTGGGGAGCTCATGGAGG
AGGTGCCTTTTCAGGAAAGGATTGTACCAAGGTGGACCGCTCAGCTGCTTATGCTGCCCGTTGGGTGGCAAAATCCCTCA
TTGAAAGAGATCTA

Alignment

ORF - retro_etel_977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.93 %
• Parental protein coverage: 77.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDTFLFTLEAVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVIINTGLVILAGKITSRAAVDYQKVV
          E.TFLFT.E.VGEGHPD.ICDQISDAVL.AHLQ.DPDAKVACETVIINTGLVILAGKITSRAA.DYQKVV
Retrocopy EGTFLFTSESVGEGHPDEICDQISDAVLYAHLQ*DPDAKVACETVIINTGLVILAGKITSRAAIDYQKVV

Parental  RDTIKHIGYDDSSKGFDYKTCALQVALEQQSPDIAQGGHLDLDQKEVGAGDYQGMVFGYAIDESEECMPL
          RDTIKHIGYDDSSKGFDYK.CA.QVALEQQSPDIAQGGHLDL..KEVGAGDYQGMVFGYA.DE.EECMPL
Retrocopy RDTIKHIGYDDSSKGFDYKACAVQVALEQQSPDIAQGGHLDLNEKEVGAGDYQGMVFGYAADETEECMPL

Parental  TLALAHQLNAKLAELRRNGTLPWLRPDSKTQVTMQYKKDQGAVLPIRVHEIVISVQHDEDVSLHEMREAL
          TL.LAHQLNAKLAELRRNGTLPWLRPDSKTQV..QY.KD.GAVLPIR.HEIV.SVQHDEDVSL.EMREAL
Retrocopy TLVLAHQLNAKLAELRRNGTLPWLRPDSKTQVAVQYMKDRGAVLPIRIHEIVMSVQHDEDVSLDEMREAL

Parental  KEKVIEVVVPTVFLDENIIYHLQPSGRFVTGGPQASTGMSGRKIIEDTYGGWGAHGGGAFSGKDCTKVDR
          KEKVI.VVVP...LDE..IYH.QPSGRFV.GGPQASTG.SG.KII.DTYGGWGAHGGGAFSGKDCTKVDR
Retrocopy KEKVIKVVVPAKYLDEDTIYHIQPSGRFVIGGPQASTGLSGQKIILDTYGGWGAHGGGAFSGKDCTKVDR

Parental  SAAYAARWVAKSLIDRDL
          SAAYAARWVAKSLI.RDL
Retrocopy SAAYAARWVAKSLIERDL

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_977 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,