RetrogeneDB ID: retro_etel_1567

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_279346:79051..79455(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT3
• Ensembl ID: ENSETEG00000007350
• Aliases: None
• Description: histidine triad nucleotide binding protein 3 [Source:HGNC Symbol;Acc:18468]

Sequence

>retro_etel_1567
ATGGCGAAGGAACCAAGTCTCCATAGTGCTCAGCCGGACCTCAACCCGGAGACAGCGGCATCTGCAAAGCCGAAGAGGTC
CCCCATGCAGTCATCAGTGGTCACTGCAGAGTCCCTGGTGCCTATGGACCACGACAGCAAGTGCATGTTCTGCTGGATCG
CGCAGGGGCAGGAACCAAGCACTGAACTTTTCTGCCCTGTGAGAATGAAGACCTACTTTGCTTCAAAGATATCAAACCAG
CAGCACCTCATCATTATCTAGTAGTGCCAAAGAAGCCTATCGGAAACTGCAAAGATCTAGAGAAGGCTCATATAGAATGG
GTTGAGAACCTGTTAGCTGTTGGAAAAGCCATCCTGCAAAGGAATAATTTCACTGACTTAAAAAATGTGAGGATGGGTTT
CCAC

Alignment

ORF - retro_etel_1567 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.79 %
• Parental protein coverage: 73.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEEPSRHATQPDLTRETAAADKPTRSPTRPSAVAAESPAPADCDSKCVFCRIA-RGQEPSTEL-LPCEN
          MA.EPS.H..QPDL..ETAA..KP.RSP...S.V.AES..P.D.DSKC.FC.IA.RG........LPCEN
Retrocopy MAKEPSLHSAQPDLNPETAASAKPKRSPMQSSVVTAESLVPMDHDSKCMFCWIA>RGRNQALNF>LPCEN

Parental  EDLVCFKDIKPAAPHHYLVVPKKHIGNCKDLEKAHLELVENMVAVGKAILERNNFTDLKNARMGFH
          EDL.CFKDIKPAAPHHYLVVPKK.IGNCKDLEKAH.E.VEN..AVGKAIL.RNNFTDLKN.RMGFH
Retrocopy EDLLCFKDIKPAAPHHYLVVPKKPIGNCKDLEKAHIEWVENLLAVGKAILQRNNFTDLKNVRMGFH

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_1567 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001830	1 retrocopy	retro_chof_38,
Callithrix jacchus	ENSCJAG00000003710	1 retrocopy	retro_cjac_3868,
Cavia porcellus	ENSCPOG00000021856	1 retrocopy	retro_cpor_674,
Echinops telfairi	ENSETEG00000007350	1 retrocopy	retro_etel_1567 ,
Macropus eugenii	ENSMEUG00000007627	1 retrocopy	retro_meug_853,
Mus musculus	ENSMUSG00000019791	1 retrocopy	retro_mmus_1387,