RetrogeneDB ID: retro_etel_1643

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_284981:364..1009(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000006005
• Aliases: None
• Description: None

Sequence

>retro_etel_1643
GAGAAGCTCAAGGAGAAGGTGGTGAAGCATGAGGACCTCTTCATCGTCAGCAAGCTGTGGCCCCCCTTCTTCGAGAGGCC
CCTGGTGAAGGAAGCCTGCCGGAAGACCCTTCAGGATCGGAAACTGGACTACCTGGACATCTACCTAATACACTGGCCTC
GGGGCCTGAAGCCTGGGAAGGAGCTCCTCCCCAAAGACGAAGCAGCCAACCTGTTCTGCAGCAAGGCAACGTTCGTGGAT
GCCTGGGAGGCCACGGAGGAGCTGGTGGATGAGGGGCTGGTGAAAGCCATTGGCGTCTCAAACTTCAACCACTTCCGGAT
TGAGAGGCTCTTGAACAAACCCGGACTGAAACACAAGCCAGTGACAAACCAGGTGGAGTGTCCCCCATGCCTCACGCAGG
AGAAGCTGATCCAGTACTGGCAGTCCAAGGGCATCACAGTCCCTGCCCACAGCCCCCTGGGCTCTCCAGACAGACCTTGG
GTCCAACCAGAGGACCCTTCGCTGCTGGAACACCCCAAGATTAAGGAGCTTGCCGCAAAGCATAACATCACTCCTGCCCA
GGTTCTGATCCGCTTCCCTATCCAGAGGAACGTGGTCGTGATCCCCAAGTCTGCGAACCCCAAACGCATTGTTGAGAACT
TCCAG

Alignment

ORF - retro_etel_1643 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.12 %
• Parental protein coverage: 78.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKLKEKVVKREDLFIVSKLWSTFFERPLVKEACRKTLNDLKLDYLDIYLIHWPQGLKPGKEILPKDEAGN
          EKLKEKVVK.EDLFIVSKLW..FFERPLVKEACRKTL.D.KLDYLDIYLIHWP.GLKPGKE.LPKDEA.N
Retrocopy EKLKEKVVKHEDLFIVSKLWPPFFERPLVKEACRKTLQDRKLDYLDIYLIHWPRGLKPGKELLPKDEAAN

Parental  LLCCKATFVDAWEAMEKLV-ERLVKAFGVSIFNHSQIERLWNKPGLKHKPVMNQVECHPYLTQEKLIQYC
          L.C.KATFVDAWEA.E.LV.E.LVKA.GVS.FNH..IERL.NKPGLKHKPV.NQVEC.P.LTQEKLIQY.
Retrocopy LFCSKATFVDAWEATEELVDEGLVKAIGVSNFNHFRIERLLNKPGLKHKPVTNQVECPPCLTQEKLIQYW

Parental  HSKGIAVTAYSPLGSPDRPWVQPEDPSLLEHPKIKEIAAKHNKTPAQVLIRFHIQRNVVVIPKSVTPKRI
          .SKGI.V.A.SPLGSPDRPWVQPEDPSLLEHPKIKE.AAKHN.TPAQVLIRF.IQRNVVVIPKS..PKRI
Retrocopy QSKGITVPAHSPLGSPDRPWVQPEDPSLLEHPKIKELAAKHNITPAQVLIRFPIQRNVVVIPKSANPKRI

Parental  VENFQ
          VENFQ
Retrocopy VENFQ

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_1643 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643 , retro_etel_748,
Echinops telfairi	ENSETEG00000006450	1 retrocopy	retro_etel_1106,
Echinops telfairi	ENSETEG00000009155	1 retrocopy	retro_etel_352,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,