RetrogeneDB ID: retro_etel_1983

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_321668:279210..279644(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR1
• Ensembl ID: ENSETEG00000020111
• Aliases: None
• Description: signal sequence receptor, alpha [Source:HGNC Symbol;Acc:11323]

Sequence

>retro_etel_1983
ATGAGACCCCTCCCCCACCTGCTTTTGCTGATCCTGCTCACTTTCCCTGCCACCCTTGTCTTTAAAAGGGGCCCTGGAGC
ATTGGCTCAGGATCTTAGAGATAATAAGAAACCATGGAAGATTCAATAAGTGAAGATGAAGATGATGAACCTGAGGTGAA
AGAAGGTGAACCCACAAATCTGGCAGATGACAAAGACGTAGACTTGTCTGGTGAACCTGAATCTTTACCATGTGCAGATA
CAACTATCCTGTCTGTAAAAGGAGAAGATTTTCCAGCAAATAATACTATGAAGTTCCTGGTTGGCTTTACAAACCAGGCT
TCAGAAGACTTTGTTATTGAATCACTCGATGCTTCTTTCCATTATCCTCATGACTACCAGGTTTATATCCAGAATTTCAC
AGCCATTCCTCTGAACTCCTTCATTCCTGCAGAG

Alignment

ORF - retro_etel_1983 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.67 %
• Parental protein coverage: 52.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLLPRLLLLLLLTFPATLLFRGGSGGSLALAQDLTEDE-ETVEDSIIEDEDDEAEVEEDEPTDLAEDKE
          MR.LP.LLLL.LLTFPATL.F..G.G...ALAQDL.....ET.EDSI.EDEDDE.EV.E.EPT.LA.DK.
Retrocopy MRPLPHLLLLILLTFPATLVFKRGPG---ALAQDLRDNK<ETMEDSISEDEDDEPEVKEGEPTNLADDKD

Parental  EEDLSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFVVESLDASFRYPQDYQFYIQNFTA
          ..DLSGEPE..P.ADTTIL.VKGEDFPANN..KFLVGFTN...EDFV.ESLDASF.YP.DYQ.YIQNFTA
Retrocopy V-DLSGEPESLPCADTTILSVKGEDFPANNTMKFLVGFTNQASEDFVIESLDASFHYPHDYQVYIQNFTA

Parental  LPLNTVVPPQ
          .PLN...P..
Retrocopy IPLNSFIPAE

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_1983 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022731	1 retrocopy	retro_btau_1285,
Dasypus novemcinctus	ENSDNOG00000015772	1 retrocopy	retro_dnov_879,
Equus caballus	ENSECAG00000019520	1 retrocopy	retro_ecab_399,
Echinops telfairi	ENSETEG00000020111	1 retrocopy	retro_etel_1983 ,
Oryctolagus cuniculus	ENSOCUG00000009083	1 retrocopy	retro_ocun_1388,
Otolemur garnettii	ENSOGAG00000014234	1 retrocopy	retro_ogar_1465,
Ictidomys tridecemlineatus	ENSSTOG00000022608	1 retrocopy	retro_itri_1850,