RetrogeneDB ID: retro_etel_707

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_149018:553..1188(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000007870
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PCGF6
• Ensembl ID: ENSETEG00000004417
• Aliases: None
• Description: polycomb group ring finger 6 [Source:HGNC Symbol;Acc:21156]

Sequence

>retro_etel_707
CTGATTAACCTCTCTGAGCTGACCCGGTATATCTTGGTTACATCTGTAAAGGTTACGTAACAGATGCTACTACCATTACC
GAGTGTCTTCAGACCTTTTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAAGAGATGTCCAAAATGCAACGTAGT
AATACATCAAACACAACCTCTTTATAACATAAGGTTGGACCGACAATTAGAAGACATAGTGTACAAATTAGTGATCGATA
TAGAGGAAAGAGAAAAAAAGCGAATGCATGATTTCTATGAAGAAAGAGATCTAGAAGTGCCTAAACTAGCTGTCCCACAA
CAGTATCTTCAAGCAAAAGAAAAATCTAAGAAAGCCCTGGAATCAGTGTTTCAGATTCCACCTGAACTTGACATGTCTTT
ATTACTGGAGTTCATTGGTGCTAATGAAGGAACGGGACATTTAAAGCCACTTGGAAAGAAGTTTGTCCGAGTTTCAGGAG
AAGCAACTACTGGTCATGTAGACAAATTCCTCAGAAGAAAAACGGGTCTGGATCCAGCTTGTGAGGCAGATAGCATCTGA
GGTGCCCACCTGTGGGAGGGGCAGTATCCCACTCTAAGAGAAATCTAACGTGCAATAGGTGATGCAGCCATGCAA

Alignment

ORF - retro_etel_707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.16 %
• Parental protein coverage: 64.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LINLSELTPYILCS-ICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQ
          LINLSELT.YIL...ICKGY..DATTITECL.TFCKSCIVRHFYYS.RCPKCN.V.HQTQPLYNIRLDRQ
Retrocopy LINLSELTRYILVT<ICKGYVTDATTITECLQTFCKSCIVRHFYYSKRCPKCNVVIHQTQPLYNIRLDRQ

Parental  LQDIVYKLVIDLEEREKKQMHDFYKERGLEVPKPAAPQPVPSSKGKSKKALESVFRIPPELDMSLLLEFI
          L.DIVYKLVID.EEREKK.MHDFY.ER.LEVPK.A.PQ.....K.KSKKALESVF.IPPELDMSLLLEFI
Retrocopy LEDIVYKLVIDIEEREKKRMHDFYEERDLEVPKLAVPQQYLQAKEKSKKALESVFQIPPELDMSLLLEFI

Parental  GANEGTGHFKPLEKKFVRVSGEATIGHVEKFLRRKLGLDPACQVDIICGDHLLE-QYQTLREIRRAIGDA
          GANEGTGH.KPL.KKFVRVSGEAT.GHV.KFLRRK.GLDPAC..D.I.G.HL.E.QY.TLREI.RAIGDA
Retrocopy GANEGTGHLKPLGKKFVRVSGEATTGHVDKFLRRKTGLDPACEADSI*GAHLWEGQYPTLREI*RAIGDA

Parental  AMQ
          AMQ
Retrocopy AMQ

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_707 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000004417	1 retrocopy	retro_etel_707 ,
Myotis lucifugus	ENSMLUG00000004985	1 retrocopy	retro_mluc_815,
Rattus norvegicus	ENSRNOG00000020250	2 retrocopies	retro_rnor_2429, retro_rnor_2430,