RetrogeneDB ID: retro_etel_2085

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_51976:1206..1686(-)
• 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_2085
GTACATTCTTTCCTGAAACAGCTGGGGAATGAGACTGCAGACATAGTACTAAAGAAGTTGATGAACAATATCAAAAGTAT
AAGTATATGGAACTCAATCTTGCACACAAAAAAAGGAGGCTAACAGGTCAGATTCCAGAAATTAAGCAGACTTTAGAAAT
GCTCAAATACATGCAGAAGAAAAAAAGAGTCCACCATTTCACTGGAGAGCAGATTCTTATTGGCAGATAACCTCTTCAGC
CAAGCTTCCATTCCTCCTACTGACCGTGTGTGTCTGTGGCCGGGGGCGAATGTAGTGCTCAGATGTGATATTGATGAAGC
TCCGGCACTGTTGGGAAAGACCTTAGCAACTGCCACAAAGAACCTTGCTTCTCTTGACTTTCTTCGAGACCAATTTACAA
CTACGATAGTCAATATGGCAAAGATTTATAATTTGGGTATAAAAATAAGAAACGAAAATGATTCTACAAGGCAAAAAGCT

Alignment

ORF - retro_etel_2085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.7 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDSFMKQPGNETADIVLKKL-DEQYQKYKFMELNLAQKKRRLKGQIPEIKQTLEILKYMQK-KKESTKSL
          V.SF.KQ.GNETADIVLKKL.DEQYQKYK.MELNLA.KKRRL.GQIPEIKQTLE.LKYMQK.KKEST.SL
Retrocopy VHSFLKQLGNETADIVLKKL<DEQYQKYKYMELNLAHKKRRLTGQIPEIKQTLEMLKYMQK>KKESTISL

Parental  ETRFLLADNLYCKASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLGTATKNLDSLEEDLDFLRDQFTT
          E.RFLLADNL...AS.PPTD.VCLW.GANV.L..DIDEA.ALL.K.L.TATKNL.SL.....FLRDQFTT
Retrocopy ESRFLLADNLFSQASIPPTDRVCLWPGANVVLRCDIDEAPALLGKTLATATKNLASLD----FLRDQFTT

Parental  TEVNMARVYNWDVKRRNKDDSIKNKA
          T.VNMA..YN...K.RN..DS...KA
Retrocopy TIVNMAKIYNLGIKIRNENDSTRQKA

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_2085 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,