RetrogeneDB ID: retro_etel_379

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_6558:17109..17718(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASF1B
• Ensembl ID: ENSETEG00000013713
• Aliases: None
• Description: anti-silencing function 1B histone chaperone [Source:HGNC Symbol;Acc:20996]

Sequence

>retro_etel_379
ATGGCCAAGGTGTTGTTGTTGAATGTGGCGGTCCTGGAGAATCTGAGTACTTTTCACAGCCCCTTCCAGTTCAAGATTAG
CTTCTAAAGCAATGAAACCTTGGAGGATAACCTGGAGTGGAAGATCATTGACGTGGGCTCCGCCGAGAGTGAGGAGTTCG
GTCAAGTCCTAGACTCGGTGCTGGTTGGCCCAGTCCCAGCAGGGAAGCACGTGTTTGTTTTTCAGGCTCATGCCCCCAAT
CTTCCCTCATCCTGGAGACTGATACTGTGGGTGTGACTGTGATGCTCACCACCTGCACTTACCATGGATGGACAGGAGTT
CATCCAAGTGGGCTACTATGTGAACAACGAGTACCCCAGCCCTGAGCTGCATAAGAACCCACCCCAGAAGCCAGGCTTCT
CTCAGCTCCAGCACAATATCTTGACGTCCAACCCGCAAGTGACCCAGTTCCACATGAACTGGGACAACAGTGCTGATCAG
CTGGAGGCTATGGACACCCAGGACCTTTCCCTGAGTGGGGGCCTCCCCTTCAGCTGCATGGCTCTCCAGGGTCTGGGCCT
CCCGGGCTGCATCCCTAGCTTCCTCCCTGAGAACTCCATGAACTGCATC

Alignment

ORF - retro_etel_379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKVSVLNVAVLENPSPFHSPFRFEISFECNEALEDDLEWKIIYVGSAESEEF-DVLDSVLVGPVPAGRH
          MAKV..LNVAVLEN.S.FHSPF.F.ISF..NE.LED.LEWKII.VGSAESEEF..VLDSVLVGPVPAG.H
Retrocopy MAKVLLLNVAVLENLSTFHSPFQFKISF*SNETLEDNLEWKIIDVGSAESEEFGQVLDSVLVGPVPAGKH

Parental  MFVFQADAPN-PSLIPETDAVGVTVVLITCTYHGQEFIR-VGYYVNNEYPSP-ELRENPPQKPDFSQLQR
          .FVFQA.APN..SLI.ETD.VGVTV.L.TCTYHG.......G.......P.P.EL..NPPQKP.FSQLQ.
Retrocopy VFVFQAHAPN<SSLILETDTVGVTVMLTTCTYHGWTGVHPSGLLCEQRVPQP>ELHKNPPQKPGFSQLQH

Parental  NILASNPRVTRFHINWDNSADDQLEAMDSQDLSLSGGLPFGCTPLKGLGLPGCIPSLLPENSMDCI
          NIL.SNP.VT.FH.NWDNSA.DQLEAMD.QDLSLSGGLPF.C..L.GLGLPGCIPS.LPENSM.CI
Retrocopy NILTSNPQVTQFHMNWDNSA-DQLEAMDTQDLSLSGGLPFSCMALQGLGLPGCIPSFLPENSMNCI

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_379 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004085	1 retrocopy	retro_btau_662,
Canis familiaris	ENSCAFG00000016482	1 retrocopy	retro_cfam_33,
Echinops telfairi	ENSETEG00000013713	1 retrocopy	retro_etel_379 ,
Myotis lucifugus	ENSMLUG00000000537	4 retrocopies	retro_mluc_1426, retro_mluc_2042, retro_mluc_2614, retro_mluc_775,
Monodelphis domestica	ENSMODG00000012099	4 retrocopies	retro_mdom_366, retro_mdom_367, retro_mdom_369, retro_mdom_688,
Sorex araneus	ENSSARG00000000534	1 retrocopy	retro_sara_552,