RetrogeneDB ID: retro_etel_1306

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_244841:4656..5257(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCID2
• Ensembl ID: ENSETEG00000013053
• Aliases: None
• Description: PCI domain containing 2 [Source:HGNC Symbol;Acc:25653]

Sequence

>retro_etel_1306
TTTCTGGTGGGTCCGTTATTTAAGATTTACTTTAAGATCAGCAAACTCCGTTCGCGCAAACCTCTCATTCGAGCAATTGA
CAGCTCAAATCTCAAAGAAGATTCTAGCATTGCACAGAGGGTGACATACAGATACTATGGTGAATGCGAGGCTATGTTTC
ATAGTGACTTTGAACAAGCTGAGGCATAGCTGTCATTTGCATTTGAGCATTGTCACCGCTCCAGTCAGAAGAACAAGAGA
ATGATTCCGATATATTTGCTTCCAGTGAAAATGCTATTGGGTCATAGGTCAACTATTGAACTTTTTAAAAAGTATTATCT
TAAGCAGTTTGCTAAGTGAGCAAAGCTGTAATGAAGGAAATCCCTTGCTACTGAATGAAGCTCTGGCAAAACATGAAACC
TTTTTTATTCGCTGTGGTATTTTCCTTATTCTTGAAAACCTGGAGATCGTCACCTACAGGAATCTTGGTAGGAAAGTGTA
TTTGTTACTCAAAACACATCAGTTGTCTCTTGGTGCTTTTCTGGTTGCCTTGAAATTTATGCAACTAGAAGATGTAGATA
TTGATGAAGTTCGGTGTATTTTGGCTAATCTCATAAACATG

Alignment

ORF - retro_etel_1306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.3 %
• Parental protein coverage: 50.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLVNQLFKIYFKINKLHLCKPLIRAIDSSNLKEDYSIAQRVTYRYYVGRKAMFDSDFKQAEEYLSFAFER
          FLV..LFKIYFKI.KL...KPLIRAIDSSNLKED.SIAQRVTYRYY....AMF.SDF.QAE..LSFAFE.
Retrocopy FLVGPLFKIYFKISKLRSRKPLIRAIDSSNLKEDSSIAQRVTYRYYGECEAMFHSDFEQAEA*LSFAFEH

Parental  CHRSSQKNKRMILIYLLPVKMLLGHMPTIELLKKYHPLQFAK-VTKAV-REGNLFLLNEALTKHETFFIR
          CHRSSQKNKRMI.IYLLPVKMLLGH..TIEL.KKY...QFAK.V.KAV..EGN..LLNEAL.KHETFFIR
Retrocopy CHRSSQKNKRMIPIYLLPVKMLLGHRSTIELFKKYYLKQFAK<VSKAV<NEGNPLLLNEALAKHETFFIR

Parental  CGIFPILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYM
          CGIF.ILE.L.I.TYRNL..KVYLLLKTHQLSL.AFLVALKFMQ.EDVDIDEV.CILANLI.M
Retrocopy CGIFLILENLEIVTYRNLGRKVYLLLKTHQLSLGAFLVALKFMQLEDVDIDEVRCILANLINM

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_1306 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013053	1 retrocopy	retro_etel_1306 ,
Macropus eugenii	ENSMEUG00000007451	1 retrocopy	retro_meug_2086,
Myotis lucifugus	ENSMLUG00000002542	3 retrocopies	retro_mluc_120, retro_mluc_231, retro_mluc_271,