RetrogeneDB ID: retro_etel_1686

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_287510:9961..10608(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMU1
• Ensembl ID: ENSETEG00000007953
• Aliases: None
• Description: smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans) [Source:HGNC Symbol;Acc:18247]

Sequence

>retro_etel_1686
ATGTCAATCAAAATCGAGTCCTCGATGTGATCCATCTCATCATGCAGTACCTGAAGGAGCACAGTTTACACCGGGCCTTA
GCCACCTTACAGGAGGAAACGACAGTGTCTTTCAATACTGTGGACAGTATTGAGAGTTTGGTGGCTGACATTAATAGCGG
TCACTGGGATACGGTTTTACAGGCTATCCAGTCGCTGAAATTGCCAGACAAAACCCTTATTGAGCTCTATGAACAGGTTG
TTCTAGAACTGATAGAGCTCTGTGAATTGGGTGCTTCCAGGTAGCCTCTGAGGCAGATGGACCCGATGATCATGTTGAAA
CAAAACCAGCCAGAGTGGTATATTCATCTGGAAAACCTCTTGGCCAGGTTCTATTTTGATCCTCGTGAGGCATACCCCGA
TGGAAGCAGCAAAGAGAAGCGAAGAGCAGCAATTGCCCAGGCCCTAGCTGGAGAAGTCAGCGTGGTCCCCCCATCTCGTC
TCATGGCATTACTGGGACAAGCTCTGAAATGGCAGCAACACCAGGGATTGCTCCTGCCCAGCAGGACCATCTATCTGTTC
CGAGGCAAAGCAGCCATGAAATATGTGGAGGAAGAAAAGTTTCCTACACAGCTGAGTAGGCACATTAAGTTTGGTCAGAA
ATCACAT

Alignment

ORF - retro_etel_1686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.78 %
• Parental protein coverage: 50.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSIEIESS-DVIRLIMQYLKENSLHRALATLQEETTVSLNTVDSIESFVADINSGHWDTVLQAIQSLKLP
          MSI.IESS.DVI.LIMQYLKE.SLHRALATLQEETTVS.NTVDSIES.VADINSGHWDTVLQAIQSLKLP
Retrocopy MSIKIESS<DVIHLIMQYLKEHSLHRALATLQEETTVSFNTVDSIESLVADINSGHWDTVLQAIQSLKLP

Parental  DKTLIELYEQVVLELIELRELGAARSLLRQTDPMIMLKQTQPERYIHLENLLARSYFDPREAYPDGSSKE
          DKTLIELYEQVVLELIEL.ELGA.R..LRQ.DPMIMLKQ.QPE.YIHLENLLAR.YFDPREAYPDGSSKE
Retrocopy DKTLIELYEQVVLELIELCELGASR*PLRQMDPMIMLKQNQPEWYIHLENLLARFYFDPREAYPDGSSKE

Parental  KRRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPPGMTIDLFRGKAAVKDVEEEKFPTQLSRHI
          KRRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLL.P..TI.LFRGKAA.K.VEEEKFPTQLSRHI
Retrocopy KRRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLLPSRTIYLFRGKAAMKYVEEEKFPTQLSRHI

Parental  KFGQKSH
          KFGQKSH
Retrocopy KFGQKSH

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_1686 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006011	2 retrocopies	retro_dord_126, retro_dord_137,
Echinops telfairi	ENSETEG00000007953	1 retrocopy	retro_etel_1686 ,
Echinops telfairi	ENSETEG00000015731	1 retrocopy	retro_etel_15,
Myotis lucifugus	ENSMLUG00000016097	1 retrocopy	retro_mluc_213,
Monodelphis domestica	ENSMODG00000003439	1 retrocopy	retro_mdom_965,