RetrogeneDB ID: retro_etel_231

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_3918:23336..23827(-)
• Located in intron of: ENSETEG00000009527

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB7
• Ensembl ID: ENSETEG00000005432
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 7 [Source:HGNC Symbol;Acc:9544]

Sequence

>retro_etel_231
GTCATCTATAAGGAAGTTCTTGGAGCAGATACAAGGGCAACGGGAGGAGTGGTTGTTGCTGACAAGAACTGTTGAAAACT
ACACTTTGTGTCTCCCAACAGTTATTGTGCTGGGACAGACACAGACATGACACCCCTGTTCCTTTCTTCCAACTTAGACC
TCCCCTCTCTCTTCACTGGCTGCCTTCCCAGAGTTGTGATGGCCAATTTCATGCTGAAGAGAATGTTTTTCAAGTATTGG
GGTTACATTGATACAACCCTAGGTTTAGGAATAGTAGATGTTACTGGGCCTCATTTCTACTGCATCTATCCTTGTGCATC
GACTAATCAATTGCCTTGTGTCACCATGGGTTCTGGTTCCTTGGCATCAATGACTGTATTTGAAGATAAATTTAGGCCAG
ATATGGAGAAGGAGGAAGCCAAGAAGCCAGTGAGCGAGGCCTCTGCGGCTGGCATCTTCATGACTTCAGCTCTGGAAGCA
ACATTGATTTA

Alignment

ORF - retro_etel_231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.01 %
• Parental protein coverage: 61.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPR
          V.YK...VLGADTRAT.G.VVADKNC.K.HF.SPN.YC.G.....DTDMT....SSNL.L.SL.TG.LPR
Retrocopy VIYKE--VLGADTRATGGVVVADKNC*KLHFVSPNSYCAGT----DTDMTPLFLSSNLDLPSLFTGCLPR

Parental  VVTANRMLKQMLFRYQGYIGAALVLGGVDVTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPD
          VV.AN.MLK.M.F.Y.GYI...L.LG.VDVTGPH.Y.IYP..ST..LP.VTMGSGSLA.M.VFEDKFRPD
Retrocopy VVMANFMLKRMFFKYWGYIDTTLGLGIVDVTGPHFYCIYPCASTNQLPCVTMGSGSLASMTVFEDKFRPD

Parental  MEEEEAKKLVSEAIGAGVF-NDLGSGSNIDL
          ME.EEAKK.VSEA..AG.F..D..SGSNIDL
Retrocopy MEKEEAKKPVSEASAAGIF<HDFSSGSNIDL

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_231 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003067	2 retrocopies	retro_btau_1722, retro_btau_983,
Echinops telfairi	ENSETEG00000005432	2 retrocopies	retro_etel_2093, retro_etel_231 ,
Homo sapiens	ENSG00000136930	1 retrocopy	retro_hsap_1303,
Gorilla gorilla	ENSGGOG00000012164	1 retrocopy	retro_ggor_1019,
Nomascus leucogenys	ENSNLEG00000017268	1 retrocopy	retro_nleu_2947,
Otolemur garnettii	ENSOGAG00000003513	1 retrocopy	retro_ogar_2828,
Pongo abelii	ENSPPYG00000019596	1 retrocopy	retro_pabe_1092,
Pan troglodytes	ENSPTRG00000021354	1 retrocopy	retro_ptro_893,
Pteropus vampyrus	ENSPVAG00000000204	2 retrocopies	retro_pvam_1271, retro_pvam_866,
Rattus norvegicus	ENSRNOG00000011732	3 retrocopies	retro_rnor_1581, retro_rnor_1582, retro_rnor_2469,
Sorex araneus	ENSSARG00000009395	1 retrocopy	retro_sara_532,
Tupaia belangeri	ENSTBEG00000009196	2 retrocopies	retro_tbel_2889, retro_tbel_751,