RetrogeneDB ID: retro_etel_1902

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_312540:124..688(-)
• 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_1902
GTCATTCTTGCCTGTGACATCCTGGAGATCGGGGCCCAGTGGAGAACCTGCGCAAGGACAGCCCCTCCCCTGAGCGATAC
ATGGCTCAGCTCAAGGGCTATTACTGTTTTTACAAGGAGCCGCTCCCTGAGTCCGCCTACACGCACCAGCTCCTGGGCCT
CAACCTCCTCTTCCTATTGTCCAGAACGGGTGGCAGAGTTCCATGCAGAGGTGGAACGGCTCCCTGCCAAGGATATCGAG
ACCAATGTCTCCATCAAGTACCTTGTGTCCCTGGAACAGGACCTGATGGAAGACAGTTGCAACGAGGTCTTCTTGGCCAA
GGGCAACATCCCTGAGAGCCATGCATTCTTTACTGACATCCTGCTGCACACAATCCTCGATGAGATCGCCGACTGCGGAG
AGAAGGCTTATGAGAAGATCCTCTTCAGCTAGGCCACCCTAGTCCTATTCTTCAACACGCCCAAGAAGATGAAGGACCAC
GCCAAGAAGTGAGGGTGGGTCGTGGGCCCCCGCAACTACTACAGCTTCACCAGCCAGCAGCAGAAGCCCAAGGACGCCAC
CATC

Alignment

ORF - retro_etel_1902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.2 %
• Parental protein coverage: 80.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LILVRDILEIGAQWSI-LRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS-QN-RVAE
          .IL..DILEIGAQW...LRKD.PS.ERYMAQLK.YY..YKE.LPESAY.HQLLGLNLLFLLS.QN.RVAE
Retrocopy VILACDILEIGAQWRT<LRKDSPSPERYMAQLKGYYCFYKEPLPESAYTHQLLGLNLLFLLS<QN<RVAE

Parental  FHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEK
          FH.E.ERLPAKDI.TNV.IK..VSLEQ.LME.S.N.VFLAKGNIP.ES..FF.DILL.TI.DEIA.C.EK
Retrocopy FHAEVERLPAKDIETNVSIKYLVSLEQDLMEDSCNEVFLAKGNIP-ESHAFFTDILLHTILDEIADCGEK

Parental  AYEKILFSEATRVLFFNTPKKMTDYAKKRGWVLGPSIYYSFASQQQKPEDTTI
          AYEKILFS.AT.VLFFNTPKKM.D.AKK.GWV.GP..YYSF.SQQQKP.D.TI
Retrocopy AYEKILFS*ATLVLFFNTPKKMKDHAKK*GWVVGPRNYYSFTSQQQKPKDATI

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_1902 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,