RetrogeneDB ID: retro_etel_2151

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_77772:91..1576(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000016022
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HP1BP3
• Ensembl ID: ENSETEG00000011454
• Aliases: None
• Description: heterochromatin protein 1, binding protein 3 [Source:HGNC Symbol;Acc:24973]

Sequence

>retro_etel_2151
ATGGCGACTGATACGTCTCAAGGTGAACTCGTCCATCCTAAGGCACTCCCACTTATAGTAGGAGCTCAGCTGATCCACGC
GGACAAGTTAGGTGAGAAGGTAGAAGATAGCACCATGCCGATTCGACGAGCTGTGAATTCTACCCGGGAAATTCCACCAA
AAAGCAAGCTTGCTGGTGGGGAGGAAGAAAAGCCAGAGCCAGACGTAAGTTCTGAGGAATCTGCCTCAACTGTAGAAGAA
CAAGAAAATGAAACTCCACCTGCGACATCTAGTGAGACGGAACAGCCCAAAGGGCAACCTGAAAATGGAGGGAAAGAAGA
AAGCAAGGCTTCTGAGGAAGCCAAACAGGATGAGAAAGATCAGTCTAAAGAAAAGGAGAAGAAAGTGAAAAAAACAATAC
CTTCCTGGGCTACCCTTTCTGCCAGCCAGCTCGCCAGAGCCCAGAAACAAACCCCAATGGCTTCTTCTCCACGGCCCAAG
ATGGATGCCATCCTAACTGAGGCCATCAAGGCATGCTTCCAGAAGAGTGGTGCATCAGTGGTTGCTATTCGAAAATATAT
CATTCATAAGTACCCTTCACTGGAGCTGGAGAGAAGGGGCTATCTCCTTAAACAAGCACTGAAGAGAGAATTAAATAGAG
GAGTTATCAAGCAGGTAAAAGGAAAAGGTGCTTCTGGGAGTTTTGTTGTGGTTCAAAAATCAAGAAAAATACTTCAGAAA
TCCAGAAACAGAAAGAAGACACCTGCAGTGGATCCAGAGCCACAAGTAAAATTGGAAGATATCCTCCCACTGGCCTTTAC
TCGCCTTTGTGAACCTAAAGAAGCTTCCTATAGTCTCATCAGAAAATATGTGTCTCAGTATTATCCTAAACTTAGAGTGG
ACATCAGGCCTCAGCTGTTGAAGAATGCTCTACAGAGGGCAGTAGAGAGAGGCCAGTTAGAACAAATAACTGGCAAAGGT
GCTTCAGGGACATTTCAGCTGAAAAATCAGGGGAGAAACCCCTGCTTGGTGGAAGCCTGATGGAATATGCCGTCTTGTCT
GCCATTGCCGCCATGAATGAGCCGAAGACCTGCTCCACCACCGCACTGAAGAAGTACGTCTTGGAGAACCACCCAGGGAC
CCATTCTAACTATCAAATGCTTCTGCTGAAGAAAACTCTGCAGAAATGTGAAAAGAATGGCTGGATGGTACAGATCTCTG
GGAAAGGATTTCGTGGCCCTTGCCAGCTCTGTGTTCCTTATCATCCCAGCCGTGGAGTTCTGTTTCCAAAGAAAGAGCCC
GAGTATTTGAAAGATGAAGGTGACGAAGAAGAAGATGAAGACTGAGGATGCGGAAATGCCTCCAAAGAGAAGGTTGCAGA
AGAAAACCCCAGCCAAGTCCCCGGGGAAAGCAGCATCCATGAAGCAAAGAGGCTCCAAGACCAGGGTTAAAGTCCCTGCT
GCCCAGAGGGGGAAAGCAAGGCCCCTGCCCAAGAAAGCCAAACCC

Alignment

ORF - retro_etel_2151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.23 %
• Parental protein coverage: 90.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATDTSQGELVHPKALPLIVGAQLIHADKLGEKVEDSTMPIRRAVNSTRETPPKSKLAGGEEEKPEPDVS
          MATDTSQGELVHPKALPLIVGAQLIHADKLGEKVEDSTMPIRRAVNSTRE.PPKSKLAGGEEEKPEPDVS
Retrocopy MATDTSQGELVHPKALPLIVGAQLIHADKLGEKVEDSTMPIRRAVNSTREIPPKSKLAGGEEEKPEPDVS

Parental  SEESASTVEEQENETPPATSSETEQPKGQPENGGKEESKASEEAKQDEKDQSKEKEKKVKKTIPSWATLS
          SEESASTVEEQENETPPATSSETEQPKGQPENGGKEESKASEEAKQDEKDQSKEKEKKVKKTIPSWATLS
Retrocopy SEESASTVEEQENETPPATSSETEQPKGQPENGGKEESKASEEAKQDEKDQSKEKEKKVKKTIPSWATLS

Parental  ASQLARAQKQTPMASSPRPKMDAILTEAIKAXACFQKSGASVVAIRKYIIHKYPSLELERRGYLLKQALK
          ASQLARAQKQTPMASSPRPKMDAILTEAIKA..CFQKSGASVVAIRKYIIHKYPSLELERRGYLLKQALK
Retrocopy ASQLARAQKQTPMASSPRPKMDAILTEAIKA--CFQKSGASVVAIRKYIIHKYPSLELERRGYLLKQALK

Parental  RELNRGVIKQVKGKGASGSFVVVQKSRKILQKSRNRKKTPAVDPEPQVKLEDILPLAFTRLCEPKEASYS
          RELNRGVIKQVKGKGASGSFVVVQKSRKILQKSRNRKKTPAVDPEPQVKLEDILPLAFTRLCEPKEASYS
Retrocopy RELNRGVIKQVKGKGASGSFVVVQKSRKILQKSRNRKKTPAVDPEPQVKLEDILPLAFTRLCEPKEASYS

Parental  LIRKYVSQYYPKLRVDIRPQLLKNALQRAVERGQLEQITGKGASGTFQLK-KSGEKPLLGGSLMEYAVLS
          LIRKYVSQYYPKLRVDIRPQLLKNALQRAVERGQLEQITGKGASGTFQLK.KSGEKPLLGGSLMEYAVLS
Retrocopy LIRKYVSQYYPKLRVDIRPQLLKNALQRAVERGQLEQITGKGASGTFQLK<KSGEKPLLGGSLMEYAVLS

Parental  AIAAMNEPKTCSTTALKKYVLENHPGTNSNYQMHLLKKTLQKCEKNGWMEQISGKGFSGTFQLCFPYYPS
          AIAAMNEPKTCSTTALKKYVLENHPGT.SNYQM.LLKKTLQKCEKNGWM.QISGKGF.G..QLC.PY.PS
Retrocopy AIAAMNEPKTCSTTALKKYVLENHPGTHSNYQMLLLKKTLQKCEKNGWMVQISGKGFRGPCQLCVPYHPS

Parental  PGVLFPKKEPEDSKDEDEDDSSEEDED-SEDEEPPPKRRLQKKTPAKSPGKAASMKQRGSKPRVKVPAAQ
          .GVLFPKKEPE..KDE......EEDED....E.P.PKRRLQKKTPAKSPGKAASMKQRGSK.RVKVPAAQ
Retrocopy RGVLFPKKEPEYLKDEGDE---EEDED>EDAEMP-PKRRLQKKTPAKSPGKAASMKQRGSKTRVKVPAAQ

Parental  RGKARPLPKKAPP
          RGKARPLPKKA.P
Retrocopy RGKARPLPKKAKP

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_2151 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011454	1 retrocopy	retro_etel_2151 ,