RetrogeneDB ID: retro_etel_1659

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_286342:102541..103114(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC1
• Ensembl ID: ENSETEG00000019397
• Aliases: None
• Description: tetratricopeptide repeat domain 1 [Source:HGNC Symbol;Acc:12391]

Sequence

>retro_etel_1659
AAGGACATGTCTGATGAAGAGAAACAGAAAAGACGAGAGGAGAGCACCCGGCTGAAGGGAGCGGGAAACGAACAGTTTAA
GAAAGGAGATTATGTTGAAGCAGAAAGCTCTTACAGTCGAGCCCTTCACACGTGTCCGGCCTGCTTCCAGACAGACAGGT
CTGTTCTGTTTTCAAATAGAGCTGCTGCAAGGATGAAACAGGACAAGAAGGAGATGGCTCTCGGTGACTGCAGCAAAGCA
ATTCAGTTAAATCCCAGCTACATTAGGGCAATACTGAGGAGAGCCGAGTTGTACGAGAAGACAGACAAACTGGATGAAGC
CTTGGAAGACTATAAATCTATATTAGAAAAAGATCCATCCATACATCAAGCAAGAGAAGCTTGTATGAGATTGCCTAAAC
AAATTGAAGAACGGAATGAAAAGCTAAAGGAAGAGATGTTAGGTAAACTAAAAGATCTTGGGAACTTGGTTCTCCGGCCT
TTTGGACTCTCCACAGAAAACTTCCAGATCAAGCAGGATTCCTCTACTGGCTCATATTCGGTCAATTTTGTTCAAAATCG
AAATAACAACAGA

Alignment

ORF - retro_etel_1659 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.34 %
• Parental protein coverage: 65.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDMSDEEKQKRREESTRLKGAGNEQFKKGDYVEAESSYSRALHTCPACFQTDRSVLFSNRAAARMKQDKK
          KDMSDEEKQKRREESTRLKGAGNEQFKKGDYVEAESSYSRALHTCPACFQTDRSVLFSNRAAARMKQDKK
Retrocopy KDMSDEEKQKRREESTRLKGAGNEQFKKGDYVEAESSYSRALHTCPACFQTDRSVLFSNRAAARMKQDKK

Parental  EMALGDCSKAIQLNPSYIRAILRRAELYEKTDKLDEALEDYKSILEKDPSIHQAREACMRLPKQIEERNE
          EMALGDCSKAIQLNPSYIRAILRRAELYEKTDKLDEALEDYKSILEKDPSIHQAREACMRLPKQIEERNE
Retrocopy EMALGDCSKAIQLNPSYIRAILRRAELYEKTDKLDEALEDYKSILEKDPSIHQAREACMRLPKQIEERNE

Parental  KLKEEMLGKLKDLGNLYLRPFGLST-NFPIEQDSSTGSYSVNFVHNQNTNR
          KLKEEMLGKLKDLGNL.LRPFGLST.NF.I.QDSSTGSYSVNFV.N.N.NR
Retrocopy KLKEEMLGKLKDLGNLVLRPFGLSTENFQIKQDSSTGSYSVNFVQNRNNNR

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_1659 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019397	1 retrocopy	retro_etel_1659 ,
Myotis lucifugus	ENSMLUG00000003057	2 retrocopies	retro_mluc_1351, retro_mluc_2408,
Otolemur garnettii	ENSOGAG00000016342	1 retrocopy	retro_ogar_1052,
Tupaia belangeri	ENSTBEG00000004641	1 retrocopy	retro_tbel_3250,
Vicugna pacos	ENSVPAG00000012031	1 retrocopy	retro_vpac_498,