RetrogeneDB ID: retro_etel_71

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_1203:72751..73205(-)
• Located in intron of: ENSETEG00000006901

Retrocopy information

• Ensembl ID: ENSETEG00000006909
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NME1
• Ensembl ID: ENSETEG00000005563
• Aliases: None
• Description: NME/NM23 nucleoside diphosphate kinase 1 [Source:HGNC Symbol;Acc:7849]

Sequence

>retro_etel_71
ACCATGGCCAACAGTGAGCACACTTTTGTCGCCATTAAGCCAGATGGCGTGCAGTGCGGCCTGGTGGGCGACATCATCAA
GCACTTTGAGCAGAAGGGCTTCTGACTGGTGGGCATGAAACTCATTCAGGCCTCCGAGGAACACATGAAGCAGCACTACG
TTGACCTGAAAGACTGCCCCTTCCTCCCAGGGCTGGTGAAGTACATGAACTCAGGACCAATTGTGCCCATGGTCTGGGAG
GGGCTGAATGTGGTGAAGACAGGCCAGGTGATGCTGGGAGAGACCAACCCAGCGGATTCTAAGCCAGGCACCATCCGAGG
GGACTTCTGTATTCAAGTTGGCAGGAACATCACTCATGGCAGTGATTTGGTCAAGGGCACCGAGAAAGAAATCAGCTTCT
GGTTTAAGCTGGAGGAACTGGTGGACCACAACTTGTTGCTATGACTGGATCTAC

Alignment

ORF - retro_etel_71 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.74 %
• Parental protein coverage: 56.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TMANSERTFIAIKPDGVQRGLVGDIIKRFEQKGFRLVGMKLVQASEEHLKQHSIDLKDRPFFPGLVKDMN
          TMANSE.TF.AIKPDGVQ.GLVGDIIK.FEQKGF.LVGMKL.QASEEH.KQH..DLKD.PF.PGLVK.MN
Retrocopy TMANSEHTFVAIKPDGVQCGLVGDIIKHFEQKGF*LVGMKLIQASEEHMKQHYVDLKDCPFLPGLVKYMN

Parental  SGPIVAMVWEGLNVVKTGRVM-GETHPADSKP--TRGDFCIQVG-NIIHGSDSVKSAEKEISLWFKPEEL
          SGPIV.MVWEGLNVVKTG.VM.GET.PADSKP...RGDFCIQVG.NI.HGSD.VK..EKEIS.WFK.EEL
Retrocopy SGPIVPMVWEGLNVVKTGQVMLGETNPADSKPGTIRGDFCIQVGRNITHGSDLVKGTEKEISFWFKLEEL

Parental  VDYK-SCCYDWIY
          VD....C.YDWIY
Retrocopy VDHN>CC-YDWIY

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_71 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 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Cavia porcellus	ENSCPOG00000008413	1 retrocopy	retro_cpor_599,
Echinops telfairi	ENSETEG00000005563	4 retrocopies	retro_etel_242, retro_etel_547, retro_etel_71 , retro_etel_803,
Echinops telfairi	ENSETEG00000014875	1 retrocopy	retro_etel_1833,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,