RetrogeneDB ID: retro_etel_1629

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_284063:3626..3870(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN1
• Ensembl ID: ENSETEG00000019281
• Aliases: None
• Description: prefoldin subunit 1 [Source:HGNC Symbol;Acc:8866]

Sequence

>retro_etel_1629
GCTAAGCTGAAAAAGCACGCACATTTTGCAGCTACAGAGGCCATGACGATGGTAGATGAGACTAACATGTCTGAAGGTAC
AGGAAGAACGTTTCTTCTTCAGGCTAAGAAGGTAATTCACAACCAGCTGCTGGAAAAACAGAAATAGCAGAGGGAAAAAA
TTAAAGAATTGGAGCACAAAAAATTCTGCCTGAGCAGAGCGTCAAGGAAGTAGAGGAGAACATCCGGAGATGCTGATGGC
AAGA

Alignment

ORF - retro_etel_1629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 67.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRTRKHAHLTDTEIMTLVDETHMYEGVGRMFILQSKEVIHNQLLEKQKIAEEKIKELEQKKSYL-ERSVK
          ....KHAH...TE.MT.VDET.M.EG.GR.F.LQ.K.VIHNQLLEKQK...EKIKELE.KK..L.E.SVK
Retrocopy AKLKKHAHFAATEAMTMVDETNMSEGTGRTFLLQAKKVIHNQLLEKQK*QREKIKELEHKKFCL<EQSVK

Parental  EAEDNIR-EMLMAR
          E.E.NIR.EMLMAR
Retrocopy EVEENIR<EMLMAR

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_1629 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 12 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005742	8 retrocopies	retro_cfam_1742, retro_cfam_1893, retro_cfam_1943, retro_cfam_251, retro_cfam_276, retro_cfam_417, retro_cfam_788, retro_cfam_997,
Equus caballus	ENSECAG00000011843	1 retrocopy	retro_ecab_53,
Erinaceus europaeus	ENSEEUG00000005357	1 retrocopy	retro_eeur_537,
Echinops telfairi	ENSETEG00000019281	1 retrocopy	retro_etel_1629 ,
Felis catus	ENSFCAG00000001272	1 retrocopy	retro_fcat_1323,
Homo sapiens	ENSG00000113068	1 retrocopy	retro_hsap_2606,
Macropus eugenii	ENSMEUG00000002726	3 retrocopies	retro_meug_380, retro_meug_686, retro_meug_801,
Microcebus murinus	ENSMICG00000000349	1 retrocopy	retro_mmur_1121,
Oryctolagus cuniculus	ENSOCUG00000009432	4 retrocopies	retro_ocun_1049, retro_ocun_1885, retro_ocun_804, retro_ocun_999,
Otolemur garnettii	ENSOGAG00000003376	6 retrocopies	retro_ogar_1025, retro_ogar_1216, retro_ogar_1412, retro_ogar_2217, retro_ogar_3129, retro_ogar_89,
Pan troglodytes	ENSPTRG00000017310	1 retrocopy	retro_ptro_1757,
Rattus norvegicus	ENSRNOG00000018653	1 retrocopy	retro_rnor_985,