RetrogeneDB ID: retro_etel_1898

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_312402:43773..44228(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX3
• Ensembl ID: ENSETEG00000002557
• Aliases: None
• Description: Y box binding protein 3 [Source:HGNC Symbol;Acc:2428]

Sequence

>retro_etel_1898
CAGTTCTTTGGGGCCTGGAGTCAGCCGTGCCACCCCCAGTATCACCCTCAGTACCGGCAGCGGCGGTTCCTGCCTTACCA
AGTGGGACAGACTTTTGACCGTCGCACTCGGGTCTTTCCCCATCCCAACAGAATTCAGGCTGGTGAGATTGGAGAGATGG
AGGATGGGGTCCCGGAGGGCCCGGTTCATCAAAATCCAACTTACCGCCCACGGTACCATAGGAGACCTCCTCGCCCCCGA
GCTCCTCCAGCTGCTGGAGAGGCTGAAGATAACGAGACTCAACAAGCAGTCAATGGTCCAAACCAGCCATCGGCTCGCCG
TGGTTCCTGGCGGCCTACAACTACCGGCGCCGCCCCCATCCACCCAATGCTCCTTCACAAGATGGCAAAGAGGTCAAGGC
AGGTCAAGTCCCAACTGAGAATCCTGCTCCAGTCACCGAGCAGAGCAGTGCTGAG

Alignment

ORF - retro_etel_1898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.12 %
• Parental protein coverage: 55.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QFFGARNQLRRPQYRPQYRQRRFPPYHVGQTFDRRTRVFPHPNRMQAGEIGEMKDGVPEGAQLQGPVHRN
          QFFGA..Q...PQY.PQYRQRRF.PY.VGQTFDRRTRVFPHPNR.QA...GE...G..E.....GPVH.N
Retrocopy QFFGAWSQPCHPQYHPQYRQRRFLPYQVGQTFDRRTRVFPHPNRIQA---GEI--GEMEDGVPEGPVHQN

Parental  PTYRPRYRSRGPPRPQALAAGKAQRNNENQQSAHGPNPPFARQ-VYPPADTYRRPLPRPNXXXXXXXXAK
          PTYRPRY..R.PPRP.A..A......NE.QQ...GPN.P.AR......A..YRR....PN.........K
Retrocopy PTYRPRYHRR-PPRPRAPPAAGEAEDNETQQAVNGPNQPSARR<WFLAAYNYRRRPHPPNAPSQDGKEVK

Parental  TGEVPTENPAPATEQSSAE
          .G.VPTENPAP.TEQSSAE
Retrocopy AGQVPTENPAPVTEQSSAE

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_1898 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002557	1 retrocopy	retro_etel_1898 ,
Echinops telfairi	ENSETEG00000004125	3 retrocopies	retro_etel_1772, retro_etel_1980, retro_etel_2134,
Microcebus murinus	ENSMICG00000004602	1 retrocopy	retro_mmur_337,
Ictidomys tridecemlineatus	ENSSTOG00000002108	1 retrocopy	retro_itri_1884,