RetrogeneDB ID: retro_etel_285

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_4743:266943..267308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSETEG00000013316
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]

Sequence

>retro_etel_285
AACCAGATAGTGGAGTTTCATAAGGAATTGGAACAGATGCCTGCTAGGGACATCCAGAAAAATGTTTACAACAAGACCCT
GTGTCTCTTGAATTGTACCCATTGGAGGGCAGTTACAAGGGCTTCCTGGCGAAGGCACCATAATTACTGAGAGCTACACC
TTCCTCATTGATATCCTGCTCGGCACTATCTGGGATAAACTTGGTAGGCTCACTGAGAAGGCCTACGGGAAGCTCCTCCT
CATTGAAGCCATCTGATCCTCTTCAACAAATCCAATACCATGATGGACCATACCAAGAAGCGATTGTGGGTCAGGGCTGC
AAAAACTTCTAAAGCGTTTCCAATAAGCAGCATAATTCAGAAGAC

Alignment

ORF - retro_etel_285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.49 %
• Parental protein coverage: 52.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NRVAEFHTELERLPAKDIQTNVYIK-HPVSLEQYLMEGSYNKVFLAK-GNIPAESYTFFIDILLDTIRDE
          N...EFH.ELE..PA.DIQ.NVY.K..PVSLE.Y..EGSY.K.FLAK.G.I..ESYTF.IDILL.TI.D.
Retrocopy NQIVEFHKELEQMPARDIQKNVYNK<DPVSLELYPLEGSY-KGFLAK<GTIITESYTFLIDILLGTIWDK

Parental  IAGCIEKAYEKILFSEAT-RVLFFNTPKKMTDYAKKRGWV-LGPSIYYSFASQQQKPED
          .....EKAY.K.L..EA....LF.N....M.D..KKR.WV..G.....S....Q...ED
Retrocopy LGRLTEKAYGKLLLIEAI<LILF-NKSNTMMDHTKKRLWV<QGCKNF*SVSNKQHNSED

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_285 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013316	3 retrocopies	retro_etel_1148, retro_etel_1902, retro_etel_285 ,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,