RetrogeneDB ID: retro_etel_1597

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_281888:2379..3093(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TGIF1
• Ensembl ID: ENSETEG00000011891
• Aliases: None
• Description: TGFB-induced factor homeobox 1 [Source:HGNC Symbol;Acc:11776]

Sequence

>retro_etel_1597
AAGAGGAGGAGAAGAGGCAACTTGCCCAAGGAACCTGTCCAGATTCTCCAGGATTGGCTGTATGAACACAGATACAATGC
TTATCTCTCAGAGCAAGAAAAAGCATTACTGTCCCAACAAACACACTTATCGACACTACAGGTCTGTAACTGGTTCATCA
ACGCCCGGCGCAGGCTCCTCCCTGACATGCTGAGAAAGGATGGCAAGGACCCCAATCAGTTCACAATTTCTCGCCGTGGG
GCCAAGATTTCTGAAGCTGACTCGTTGGAGTCCGTAATGGGCATCAAAAACTACATGCCAGCTTTGGAGGAGAGTGTGTT
TCATTCCTGTACAGCTGGACCAAGCCCCACCGTCGGCAGGCCACTTTCTCCTAAACCACCATCCCCGGGATCAATTTTGG
CTCGGCCATCAGTGATCTGCCATACCACGGTGACTGCATCGAAAGATGTGTCTTTTTCGCTCTGCCAGTCAGTAGGTGTG
GGACAAAACACAGATCTACAGCAGATGGCAGCCAGCAACTTTACAGACACCTCTCTCATGTACCCAGAGGACAGCTGCCA
ATCAGGACCAAGGACGAATACACAAAGTGGTCTTTTCAACACTCCTCCCCCCACCCCACCGGACCGCAACCAGGATTTCA
GTGGCTTTCAGCTCCTAGTGGACGTTGCACTCAAACGGGCTGCAGAGACGGAGCTTCAGGCAAAACTGATGGCT

Alignment

ORF - retro_etel_1597 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 89.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRRRRSHLPKESVQI-RDWLY-HRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDGKD
          KRRRR..LPKE.VQI..DWLY.HRYNAY.SEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDGKD
Retrocopy KRRRRGNLPKEPVQILQDWLYEHRYNAYLSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDGKD

Parental  PNQFTISRRGAKISEANSVESVMGIKNYMPALEESVFHSCTAGPSPTVGRPLSPKPPSPGSNLARPSVIC
          PNQFTISRRGAKISEA.S.ESVMGIKNYMPALEESVFHSCTAGPSPTVGRPLSPKPPSPGS.LARPSVIC
Retrocopy PNQFTISRRGAKISEADSLESVMGIKNYMPALEESVFHSCTAGPSPTVGRPLSPKPPSPGSILARPSVIC

Parental  HTTVTASKDMSFSLCQSVGVGTNTDLQQMAAQHFTDTFLMLPEGTCQSGPSTNTQSGLFSTPPPTPPDLK
          HTTVTASKD.SFSLCQSVGVG.NTDLQQMAA..FTDT.LM.PE..CQSGP.TNTQSGLF.TPPPTPPD..
Retrocopy HTTVTASKDVSFSLCQSVGVGQNTDLQQMAASNFTDTSLMYPEDSCQSGPRTNTQSGLFNTPPPTPPDRN

Parental  E----FQLLVDVALKRAAELEPQTKLMA
          .....FQLLVDVALKRAAE.E.Q.KLMA
Retrocopy QDFSGFQLLVDVALKRAAETELQAKLMA

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_1597 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000162	1 retrocopy	retro_chof_1055,
Echinops telfairi	ENSETEG00000011891	1 retrocopy	retro_etel_1597 ,