RetrogeneDB ID: retro_etel_2095

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_54691:435..1019(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RTFDC1
• Ensembl ID: ENSETEG00000003143
• Aliases: None
• Description: replication termination factor 2 domain containing 1 [Source:HGNC Symbol;Acc:15890]

Sequence

>retro_etel_2095
AAGGGCAACGCCAAAGGGACAAGCACGATGACCTCCAGCGAGCACGCGTCATCTGCCCTGGGGTGGGCTTGGAGATGCAC
GGCCCGCACAGCTTTGGCTTCTTGCGCTGCTGCGCATGTGTCTTCTCAGAGCTAGCCCTAAAGGAGATCAAGGCCGAAGT
CTGCCACACTTGTGGGACCGCCTTCCAGGAGGACGACATCTTTGTGCTCAATGGCACCAAGGGGGACCTGGAGCTGCTGA
AGACCCCTATGGAGGAGAGGCAGCTGCGTGCCAAGCTGGGAAAGAAAACAAAGAAACCCAAGGCAGCAGGGACTGTGTCA
AAGCCAGGTGTCCCTGAAGAAGGTGCGGGGCCATCTGCTGTCAGGAGCAGGAAGCCCGAGGAAATGAACCTTGACTCCAA
GGAGAAAAAGGCTGGCCTGGCTCCCAAAGGCACAGCACCGGGTGGGAGTGCATCTGGGAAAGCCGGGAAGGCTCCATGTG
CAGACACGAAGCCGACCATCGCCTACAGTCACCAGCCTGAGACCCACAAGTCCCTCTTCACGTCTCACAGCTCCGCCACG
CGCTCGAAGGAGGAGTCAGCCCAC

Alignment

ORF - retro_etel_2095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 63.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGSTKG-DKHDDLQRARFICPVVGVEMNGRHRFCFLRCCGCVFSERALKEIKAEVCHTCGAAFQEHDVIV
          KG..KG.DKHDDLQRAR.ICP.VG.EM.G.H.F.FLRCC.CVFSE.ALKEIKAEVCHTCG.AFQE.D..V
Retrocopy KGNAKG<DKHDDLQRARVICPGVGLEMHGPHSFGFLRCCACVFSELALKEIKAEVCHTCGTAFQEDDIFV

Parental  LNGTKGDVELLKARMEERRLRAKLGKKTKKPKAAETVSKPDVPEESTGPSAVTGGKPEETSLDSRE-KAG
          LNGTKGD.ELLK..MEER.LRAKLGKKTKKPKAA.TVSKP.VPEE..GPSAV...KPEE..LDS.E.KAG
Retrocopy LNGTKGDLELLKTPMEERQLRAKLGKKTKKPKAAGTVSKPGVPEEGAGPSAVRSRKPEEMNLDSKEKKAG

Parental  LVPKGPAPGGSASGKAGKAPCAAMKRPIDDSHQSETYKSLFTSHSSAKRSKEESAH
          L.PKG.APGGSASGKAGKAPCA..K..I..SHQ.ET.KSLFTSHSSA.RSKEESAH
Retrocopy LAPKGTAPGGSASGKAGKAPCADTKPTIAYSHQPETHKSLFTSHSSATRSKEESAH

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_2095 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027390	1 retrocopy	retro_btau_1076,
Echinops telfairi	ENSETEG00000003143	1 retrocopy	retro_etel_2095 ,
Mus musculus	ENSMUSG00000027502	1 retrocopy	retro_mmus_339,
Ornithorhynchus anatinus	ENSOANG00000009249	1 retrocopy	retro_oana_124,
Otolemur garnettii	ENSOGAG00000004444	1 retrocopy	retro_ogar_3150,