RetrogeneDB ID: retro_etel_1804

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_299332:111874..112140(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHIC2
• Ensembl ID: ENSETEG00000004296
• Aliases: None
• Description: cysteine-rich hydrophobic domain 2 [Source:HGNC Symbol;Acc:1935]

Sequence

>retro_etel_1804
GCGAATTTCCACGCGGTCTAGGAGGACGAGGACGAGGAGGGGACCCTGAAGGAGCAGCTGCTCAGGTACTGGTTGATCGT
GGTGATCCGCGGCTCTGGTCACGTCACCGTATTTAGACTAAGCCACAAATTAGAATCAGAACGCCCCTCTTCATGAATTG
GAAAGGTAGCTCCTGACGAATTTAAATCCAGTATCAACAGAGGGAGCAGTGGTCTTACAAGAACCTCCCTGTTCGTTCCA
GGACCTGGACCCAAGGGTGGGACTGT

Alignment

ORF - retro_etel_1804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.44 %
• Parental protein coverage: 54.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADFDIYEEEEDEERALEELLLYSPDQVVVLGSAHVSVFGLSNKFESEFPSSLTGKVAPEEFKASINRVNS
          A.F....E.EDEE..L.E.LL.....VV..GS.HV.VF.LS.K.ESE.PSS..GKVAP.EFK.SINR..S
Retrocopy ANFHAV*EDEDEEGTLKEQLLRYWLIVVIRGSGHVTVFRLSHKLESERPSS*IGKVAPDEFKSSINRGSS

Parental  CLK-KNLPINVRWLLCGCLC
          .L..KNLP...R....G..C
Retrocopy GLT<KNLPVRSRTWTQGWDC

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_1804 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000004296	1 retrocopy	retro_etel_1804 ,
Latimeria chalumnae	ENSLACG00000006603	1 retrocopy	retro_lcha_22,
Loxodonta africana	ENSLAFG00000012248	1 retrocopy	retro_lafr_953,
Macaca mulatta	ENSMMUG00000006382	1 retrocopy	retro_mmul_1372,