RetrogeneDB ID: retro_etel_1874

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_310110:163778..164445(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TWISTNB
• Ensembl ID: ENSETEG00000019157
• Aliases: None
• Description: TWIST neighbor [Source:HGNC Symbol;Acc:18027]

Sequence

>retro_etel_1874
ATTGAAGCTGATTTTGTTATTTTCTGCCCTGAACCAGGACAAAAACTTGTGGGCACAGTTAATAAAGTGTCTTCCAGCCA
CATCGGCTGTTTAGTCCATGGCTGTTTCAATGCCTCTATCCCTAAACCGGAGCAGATGCCACCTGAGCAGAGGCAAACCC
TGGAGATAAGTGTGGGAGATGAACTTGAATTTGAAGTCTTCCGCTTAGACTCTGATGCGGCTGGAGTCTTTTGCATTCGA
GGAAAACTAAACGTGGCCAGTTTGCAAGCCAAGTGTTCTCAAGTTTCTGAAGAAGCAACAGAAACCACCACTGAAGAAAC
TGTTGAAAATCCTCCACAGAAAAAGCAGAAAGGCCTAGAGACGTCCAGAGAGGGAGAGGCTGCCGCAGAGCTGGTAGCTG
TCTTGGTAAAGGGAGATGCCGGGCTGCAGACCAATGGCAGTGCAGAGGGCCTCGGTGGGGAGCAGCCCCAGGAGAAGAAG
AAGGAGAGGAAGAAGAGAAAGTCCCGGGAAGCTCCGGATCCAGACCCTGTTCTCCCAGGCAGTGACTCCAGCGGCTACCA
AAGTGACCGCAAAAAGAAGAAGAAGAAACGAAAATACGAGGAGGCAGCGGTTTCCCCCAATGTGGAACACTCACCTAAAA
AGAAAAGGAAACCGTAATCTTCCTGAA

Alignment

ORF - retro_etel_1874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.27 %
• Parental protein coverage: 65.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IEADFVIFCPEPGQKLVGTVNKVSSSHIGCLVHGCFNASIPKPEQMPPEQWQTLEISVGDELEFEVFRLD
          IEADFVIFCPEPGQKLVGTVNKVSSSHIGCLVHGCFNASIPKPEQMPPEQ.QTLEISVGDELEFEVFRLD
Retrocopy IEADFVIFCPEPGQKLVGTVNKVSSSHIGCLVHGCFNASIPKPEQMPPEQRQTLEISVGDELEFEVFRLD

Parental  SDAAGVFCIRGKLNVASLQAKCSQVSEEATETTTEETVENPPQKKKKNLETSREGEAAAELVAVLVKGDA
          SDAAGVFCIRGKLNVASLQAKCSQVSEEATETTTEETVENPPQKK.K.LETSREGEAAAELVAVLVKGDA
Retrocopy SDAAGVFCIRGKLNVASLQAKCSQVSEEATETTTEETVENPPQKKQKGLETSREGEAAAELVAVLVKGDA

Parental  GLQTNGSAEGLGGEQPQEKKKERKKRKSREAPDPDPVLPGSDSSGYQSDRKKKKKKRKYEEAAVSPNVEH
          GLQTNGSAEGLGGEQP...........SREAPDPDPVLPGSDSSGYQSDRKKKKKKRKYEEAAVSPNVEH
Retrocopy GLQTNGSAEGLGGEQPXXXXXXXXXXXSREAPDPDPVLPGSDSSGYQSDRKKKKKKRKYEEAAVSPNVEH

Parental  SP-KRKGNRNLPE
          SP.KRKGNRNLPE
Retrocopy SP>KRKGNRNLPE

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_1874 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	ENSETEG00000019157	1 retrocopy	retro_etel_1874 ,
Microcebus murinus	ENSMICG00000017730	2 retrocopies	retro_mmur_1403, retro_mmur_1427,
Mus musculus	ENSMUSG00000020561	1 retrocopy	retro_mmus_1516,