RetrogeneDB ID: retro_etel_734

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_156666:1073..1628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFB1M
• Ensembl ID: ENSETEG00000005709
• Aliases: None
• Description: transcription factor B1, mitochondrial [Source:HGNC Symbol;Acc:17037]

Sequence

>retro_etel_734
GGGCCTTTTGTTTACGGCAGGATGCAGATGACTTTGACCTTTCAAAAGGAGGTGGCAGAGAGGCTGACGGCCACCACGGG
CAGCAAGCAGCGGAGCCGTCTCTCCATCATGGCCCAGTACTTGTGCAGCGTCCAGCATGTCCTGACCATCCCCGGCCAGG
CCTTTATCCCCAAACCAGAGGTGGACGTGGGCCTAGTGCACTTCATCCCCCTGGTCCGGCCCGCCATCCAGCAGCCCTTC
GACCTGGTGGAGAAAGTGGTCCAGCACGTGTTTCAGTTCCGAAGGAAGTACTGCTACCACGGCCTGGGAATGTTGTTTCC
TGAAGATCAGCGCTTAGAAAGCACTGGAAGGCTGCTGCAGCTGGCTGATGTGGAGCCCACACTCCGGCCCTGCCAGCTGT
CCCTCGCCCACTTCAGAAGCCTCTGCGACGTGTACCGAGGAATGTGTGATGGAGACCCGCAGCTCTTCGCCTATAACTTC
CGAGAAGAACTCAAGCAGAATAAAAGCCGAAGCCAGAAGGCCCGGGAGGCCCGGGGAGCTTTGAGGCTTTCACAG

Alignment

ORF - retro_etel_734 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.89 %
• Parental protein coverage: 52.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLFVYGRTQMTLTFQKEVAERLTASTGSKQRSRLSIMAQYLCSVQHVLTIPGQAFIPKPEVDVGLVHFVP
          G.FVYGR.QMTLTFQKEVAERLTA.TGSKQRSRLSIMAQYLCSVQHVLTIPGQAFIPKPEVDVGLVHF.P
Retrocopy GPFVYGRMQMTLTFQKEVAERLTATTGSKQRSRLSIMAQYLCSVQHVLTIPGQAFIPKPEVDVGLVHFIP

Parental  LVWLTIQQLFDLVEKVVQHVFHFRRKYCYRGLGMLFPEDRRLESTGRLLQLADVEPTLRPCQLSLAHFRS
          LV...IQQ.FDLVEKVVQHVF.FRRKYCY.GLGMLFPED.RLESTGRLLQLADVEPTLRPCQLSLAHFRS
Retrocopy LVRPAIQQPFDLVEKVVQHVFQFRRKYCYHGLGMLFPEDQRLESTGRLLQLADVEPTLRPCQLSLAHFRS

Parental  LCDVYRGMCDGDPQLFAYNFREELKQNKSRSREAREP-GALRLSQ
          LCDVYRGMCDGDPQLFAYNFREELKQNKSRS..ARE..GALRLSQ
Retrocopy LCDVYRGMCDGDPQLFAYNFREELKQNKSRSQKAREARGALRLSQ

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_734 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	ENSETEG00000005709	1 retrocopy	retro_etel_734 ,
Echinops telfairi	ENSETEG00000020059	1 retrocopy	retro_etel_34,
Macropus eugenii	ENSMEUG00000001699	1 retrocopy	retro_meug_1770,
Tursiops truncatus	ENSTTRG00000006327	1 retrocopy	retro_ttru_963,