RetrogeneDB ID: retro_etel_84

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_1417:24951..25401(-)
• Located in intron of: ENSETEG00000007559

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRTFDC1
• Ensembl ID: ENSETEG00000012241
• Aliases: None
• Description: phosphoribosyl transferase domain containing 1 [Source:HGNC Symbol;Acc:23333]

Sequence

>retro_etel_84
GAACGGCTGGCTCGATATGCGATGAAGAAGGTAGGAGGCCATCCCATCGTGGCCCTCTGTGTGCTCAAGGGGGGCTAGAA
ATTCTTCGTTGACCTGCTGGATTACATCAAAGCACCGAACAGAAATAGTGACGGGTCCATTCCTATGACTGTAGATTTTA
TCGGCCTGAAGAGCGACTGTAATGACCAGTCAACTGGGGACATAAAAGTAATTGGTGGAGACAATCTCTCAACTTTGACC
GGAAAGAATGTCCTGGTTGTTGAGGAGATCATCGACACTGGCCAACCTTTGCAAACCCTGCCCTCCCAGGTCAAGCAGCA
TGACCCAAAGATGGTCAAGGTTGCCAGCTTCCTGGTGAAAAGGACTCCTTGAAGTGTTGGCTATAGACCAGCCTTTGTTG
GCTTTGACATTCTAGACAAGTTTGTGGTAGGATATGCCCTAGACTTGAAT

Alignment

ORF - retro_etel_84 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.67 %
• Parental protein coverage: 86.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERLAKDIMKDIGYCDIMVLCVLKGGYKFCADLVEHLKNISRNSDTFVSMKVDFIRLKSYRNDQSTDEMQI
          ERLA...MK..G...I..LCVLKGG.KF..DL....K...RNSD....M.VDFI.LKS..NDQST.....
Retrocopy ERLARYAMKKVGGHPIVALCVLKGG*KFFVDLLDYIKAPNRNSDGSIPMTVDFIGLKSDCNDQSTGDIKV

Parental  IGGDDLSALAGKXXXXXXDVVGTGRTMKALLGSIEKYKPNMVKVASLLVKRTPRS-SFKPDYAGFEIPDL
          IGGD.LS.L.GK..........TG.....L........P.MVKVAS.LVKRTP.S....P...GF.I.D.
Retrocopy IGGDNLSTLTGKNVLVVEEIIDTGQPLQTLPSQVKQHDPKMVKVASFLVKRTP*SVGYRPAFVGFDILDK

Parental  FVVSYALDYN
          FVV.YALD.N
Retrocopy FVVGYALDLN

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_84 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000012241	1 retrocopy	retro_etel_84 ,
Macropus eugenii	ENSMEUG00000000136	3 retrocopies	retro_meug_1887, retro_meug_2035, retro_meug_295,
Ochotona princeps	ENSOPRG00000016040	2 retrocopies	retro_opri_168, retro_opri_419,