RetrogeneDB ID: retro_etel_552

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_9002:9707..10001(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VBP1
• Ensembl ID: ENSETEG00000017655
• Aliases: None
• Description: von Hippel-Lindau binding protein 1 [Source:HGNC Symbol;Acc:12662]

Sequence

>retro_etel_552
ACCAATTCACTGGCAGCCACATGGTGACTGGCAGCTACCCTGCACTGAAAAGCTTCCCGTTCCTCCTGCTGATAAAGTGT
GCCTGTGGTTGGCAGCGATGTAATACTTGAAGATGATATTCCTGAAGCCTGGGCACTGTTGGAAAAGAATTTATCAACTG
CCACAAAGAATCTTGATTCTCTTGAAGAAGACCTGGACTTTCTTTGAGATCAGATTACTACCACAGAAGTCAATATGGCC
AAGGACGATGATTGGGATGTATAAAGACGATCCCACTGAGAGCAAAGCATCAAG

Alignment

ORF - retro_etel_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68. %
• Parental protein coverage: 58.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TKSLETRFLLADNLYCKAS-VPPTDKVCLWL-GANVMLEYDIDEAQALLEKNLGTATKNLDSLEEDLDFL
          T.SL.....LA..L..KAS.VPP.DKVCLWL.G..V.LE.DI.EA.ALLEKNL.TATKNLDSLEEDLDFL
Retrocopy TNSLAATW*LAATLH*KAS>VPPADKVCLWL<GSDVILEDDIPEAWALLEKNLSTATKNLDSLEEDLDFL

Parental  RDQFTTTEVNMARVYNWDVKRRNK-DDSIK
          .DQ.TTTEVNMA....WDV.RR.....SIK
Retrocopy *DQITTTEVNMAKDDDWDV*RRSH*EQSIK

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_552 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013652	1 retrocopy	retro_cpor_466,
Echinops telfairi	ENSETEG00000017655	2 retrocopies	retro_etel_2085, retro_etel_552 ,
Latimeria chalumnae	ENSLACG00000016144	1 retrocopy	retro_lcha_18,
Loxodonta africana	ENSLAFG00000016507	2 retrocopies	retro_lafr_1200, retro_lafr_163,
Myotis lucifugus	ENSMLUG00000015396	3 retrocopies	retro_mluc_1600, retro_mluc_2019, retro_mluc_986,
Macaca mulatta	ENSMMUG00000015095	1 retrocopy	retro_mmul_124,
Oryctolagus cuniculus	ENSOCUG00000017448	2 retrocopies	retro_ocun_233, retro_ocun_747,
Sarcophilus harrisii	ENSSHAG00000002823	1 retrocopy	retro_shar_7,