RetrogeneDB ID: retro_etel_1962

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_320066:24604..25210(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000010191
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IL6
• Ensembl ID: ENSETEG00000001221
• Aliases: None
• Description: interleukin 6 (interferon, beta 2) [Source:HGNC Symbol;Acc:6018]

Sequence

>retro_etel_1962
ACCTTCAGTCCAGTCGCCTTCTCCCTGGGGCTTCTCCTGATGATGGCTTCTGCATTCCCTACTCCGAGACCCCTGGAAGG
AGATTCTAAAGGTGATGCCATCTCAGACACACCACGCACCTCTTCAAAAGAAATTCTGGACGTCCTGATGTCCACTCTCT
CCCAAGTCGAGGAACTGAGAAAGGAGATATGTGATAAATATGACAAATGTGAAAACAGCAGGAGAGCACTGGCAGAAAAC
AATCTGAACCTTCCAAAGATGAGAGAAGAAGACAGATGCTTCCAAGATGGATTCAACAAGGAGACTTGCCTGAGGAGAAT
CATCACTGGCCTTTCACAGTTCCACAGCTACATGAAATTCGTGGGGAACACTTTGGAAGAAGAGAACAGAAAGCTCTCAG
GTGTGCTGAAGAGCATCAAAGCACTGATCCAGCTCCTGAAGGAAAACCATCCAAATGAAATAGCCACCCCTGACCCAACC
ACAAGTGCCACTGAGCTGCCCACGTGGCAGGTAAACATCAAGTGGCTGAAGAATACAACGATTAACCTCAGCCTTCAAAG
CTTGGAGAAGTTCATTCAGTTCAGCGTGAGGGCTGTTCGGCTAATG

Alignment

ORF - retro_etel_1962 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TFSPVAFFLGLLLMMASAFPTPRPLEGDSKGDAISDTPRTSSNKTLELLMFILSQVEELRKEICDKYDKC
          TFSPVAF.LGLLLMMASAFPTPRPLEGDSKGDAISDTPRTSS...L..LM..LSQVEELRKEICDKYDKC
Retrocopy TFSPVAFSLGLLLMMASAFPTPRPLEGDSKGDAISDTPRTSSKEILDVLMSTLSQVEELRKEICDKYDKC

Parental  ENSREALAENNLNLPKMREEDRCFQDGFNKETCLRRIIAGLSQFHIYMKFVGNFGRGE-QKASGVLKSIK
          ENSR.ALAENNLNLPKMREEDRCFQDGFNKETCLRRII.GLSQFH.YMKFVGN....E..K.SGVLKSIK
Retrocopy ENSRRALAENNLNLPKMREEDRCFQDGFNKETCLRRIITGLSQFHSYMKFVGNTLEEENRKLSGVLKSIK

Parental  ALIQLLEENVKHPNEIATLDSTTNATVLPTWQLNTEWLKNTMINLILQSLEKFIQFSVRAVRLM
          ALIQLL.EN..HPNEIAT.D.TT.AT.LPTWQ.N..WLKNT.INL.LQSLEKFIQFSVRAVRLM
Retrocopy ALIQLLKEN--HPNEIATPDPTTSATELPTWQVNIKWLKNTTINLSLQSLEKFIQFSVRAVRLM

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_1962 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000001221	1 retrocopy	retro_etel_1962 ,
Otolemur garnettii	ENSOGAG00000004177	1 retrocopy	retro_ogar_915,