RetrogeneDB ID: retro_etel_961

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_191646:2273..2484(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHFM1
• Ensembl ID: ENSETEG00000019778
• Aliases: None
• Description: split hand/foot malformation (ectrodactyly) type 1 [Source:HGNC Symbol;Acc:10845]

Sequence

>retro_etel_961
ATGTCCGAGAAAAAGCAGCCGGTAGACTTGAATCCTTGTGGAGGAGGAGGAGGAGTTGGAGGAGCTCCCTGTCGAAGACT
GGGCTGCCTTAGATGAAGATGGAGATGCACCTGTCTGGGAGGATCACTGGGATGAGGACAGCGCAGACGATGACTTCTCC
AGTCAGTTAGGCGCTGAATTAGAGAAACATGGCTATAAGATAGAGACTTCC

Alignment

ORF - retro_etel_961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSEKKQPVDLG-LLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAELEKHGYKMET
          MSEKKQPVDL..L..........P.EDWA.LDED.DA.VWED.WD.D...DDFS.QL.AELEKHGYK.ET
Retrocopy MSEKKQPVDLN>LXXXXXXXXXLPVEDWAALDEDGDAPVWEDHWDEDSADDDFSSQLGAELEKHGYKIET

Parental  S
          S
Retrocopy S

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_961 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002179	1 retrocopy	retro_cfam_1174,
Cavia porcellus	ENSCPOG00000010402	1 retrocopy	retro_cpor_446,
Echinops telfairi	ENSETEG00000019778	1 retrocopy	retro_etel_961 ,
Felis catus	ENSFCAG00000023254	2 retrocopies	retro_fcat_1138, retro_fcat_121,
Myotis lucifugus	ENSMLUG00000014208	1 retrocopy	retro_mluc_948,
Oryctolagus cuniculus	ENSOCUG00000026246	3 retrocopies	retro_ocun_1324, retro_ocun_452, retro_ocun_77,