RetrogeneDB ID: retro_etel_1235

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_232729:414..796(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAPB
• Ensembl ID: ENSETEG00000017229
• Aliases: None
• Description: VAMP (vesicle-associated membrane protein)-associated protein B and C [Source:HGNC Symbol;Acc:12649]

Sequence

>retro_etel_1235
ATGGTGAAGCATGAGCAAATCCTGGTCATTGACCTGACCACAGACCTCACATGTAAAGGATCCTTCACCAATGTAGTCAC
TACAAATCCTAAATTGAGAAATCCATCAGCTACAAAAGTGTGTTTTAAAGTGAAGACTACAGCTCCTCCTCGGGTCTATG
TGAGGCCCAACAGGGGACTTATTGACCCGGGGTCATCTATTACTACTTCAGTTATGCCTTTAACTATGATCCGAATAAGA
GTAGACATAAGTTTATGGCACAGACAATTTCTACTTCAACAACCACTTCCGTTATGGAAGCTTTGTGTAAAGAGGCAAAG
ACTGATAAATTAATAGATCTAAATTGAGATGTGTATTTGAAATACCCAATGAGAATGATAAA

Alignment

ORF - retro_etel_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 53.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGVIDAGASINVS
          M.K.EQ.L.......L...G.FT.VVTTN.KL.NP....VCFKVKTTAP.R..VRPN.G.ID.G.S....
Retrocopy MVKHEQILVIDLTTDLTCKGSFTNVVTTNPKLRNPSATKVCFKVKTTAPPRVYVRPNRGLIDPGSS--IT

Parental  VMLQP-FDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMD-SKLRCVFELPAENDK
          ....P.F.YDPN.KS.HKFM.Q.....T.TS.MEA..KEAK...L.D.SKLRCVFE.P.ENDK
Retrocopy TSVMP<FNYDPN-KSRHKFMAQTISTSTTTSVMEALCKEAKTDKLID<SKLRCVFEIPNENDK

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_1235 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000017229	1 retrocopy	retro_etel_1235 ,
Macropus eugenii	ENSMEUG00000009788	1 retrocopy	retro_meug_842,
Monodelphis domestica	ENSMODG00000016549	1 retrocopy	retro_mdom_919,
Nomascus leucogenys	ENSNLEG00000009351	1 retrocopy	retro_nleu_55,