RetrogeneDB ID: retro_etel_2022

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_33155:603..1160(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000015835
• Aliases: None
• Description: None

Sequence

>retro_etel_2022
GCAACTGATCAGAAACAGAAATCCATCCTGTATGAGCAGTGAAGTATCCACACAGTGAAACCCATCACCAAGCACAGAGG
CTTGGTATATACTGGTGTAGGCCCAGATTAAAGGGTACTTGTACACAGAACCCGGAATTAGCTCAGCAGTGCTAGCTGGT
TTACCAAGAGCCTATTCCCACAGTGCAGTTGGTACAAAGAATAGCTTCTTTCATGCAAGAATACACCCAGTCAGGTGGTG
TATGTCCATTTGGAGTTTCTTTATGAATTTGTGGTTGGAATGAGGGGTGACCTGATTTATTTCAGTCAGGCCCATTTGGC
GCTTACTTTGCCTGAAAAGCCACAGTAATGGGAAAGAATGATGTGAATGGGGAATTTTTCCTGGAAAGGAGATATAATAA
AGACCTGGAATTTGAAGAGGCCATTCATACAGCCAGCTTGCCCTTAAAGGAAAGCTTTGAAGGACAAATGAAAGAAGATG
ATGTAGCAGTTGGAATCTTCAATGAAGCTGCACTTAGGAGGCTGATCCCAGCGGACGTTAACGACTGCTTGGCTGCC

Alignment

ORF - retro_etel_2022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.8 %
• Parental protein coverage: 79.49 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ATEKKQKSILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRAR-KLAQQYYLVYQEPIPTAQLVQRVA
          AT..KQKSILY...S.H.V.PITKH.GLVY.G.GPD.RVLVHR.R..LAQQ..LVYQEPIPT.QLVQR.A
Retrocopy ATDQKQKSILYEQ*SIHTVKPITKHRGLVYTGVGPD*RVLVHRTR<ELAQQC*LVYQEPIPTVQLVQRIA

Parental  SVMQEYTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLELE
          S.MQEYTQSGGV.PFGVSL.ICGWNEG.P.LFQS.P.GAYFA.KAT.MGKN.VNG..FLE.RYN.DLE.E
Retrocopy SFMQEYTQSGGVCPFGVSL*ICGWNEG*PDLFQSGPFGAYFA*KATVMGKNDVNGEFFLERRYNKDLEFE

Parental  DAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAA
          .AIHTA.L.LKESFEGQM.ED...VGI.NEA..RRL.P..V.D.LAA
Retrocopy EAIHTASLPLKESFEGQMKEDDVAVGIFNEAALRRLIPADVNDCLAA

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_2022 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 24 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009433	3 retrocopies	retro_amel_1029, retro_amel_1336, retro_amel_1379,
Bos taurus	ENSBTAG00000000990	3 retrocopies	retro_btau_296, retro_btau_384, retro_btau_889,
Choloepus hoffmanni	ENSCHOG00000000644	1 retrocopy	retro_chof_893,
Callithrix jacchus	ENSCJAG00000007730	4 retrocopies	retro_cjac_1096, retro_cjac_1868, retro_cjac_2583, retro_cjac_852,
Cavia porcellus	ENSCPOG00000013134	1 retrocopy	retro_cpor_1512,
Dasypus novemcinctus	ENSDNOG00000011910	2 retrocopies	retro_dnov_2202, retro_dnov_724,
Echinops telfairi	ENSETEG00000015835	2 retrocopies	retro_etel_1569, retro_etel_2022 ,
Homo sapiens	ENSG00000106588	2 retrocopies	retro_hsap_2199, retro_hsap_908,
Gorilla gorilla	ENSGGOG00000006538	1 retrocopy	retro_ggor_735,
Myotis lucifugus	ENSMLUG00000010086	2 retrocopies	retro_mluc_1050, retro_mluc_135,
Macaca mulatta	ENSMMUG00000022451	2 retrocopies	retro_mmul_1114, retro_mmul_923,
Mustela putorius furo	ENSMPUG00000018145	1 retrocopy	retro_mputfur_548,
Mus musculus	ENSMUSG00000015671	4 retrocopies	retro_mmus_1104, retro_mmus_1105, retro_mmus_1215, retro_mmus_1320,
Nomascus leucogenys	ENSNLEG00000003177	1 retrocopy	retro_nleu_329,
Oryctolagus cuniculus	ENSOCUG00000012092	1 retrocopy	retro_ocun_774,
Otolemur garnettii	ENSOGAG00000016805	1 retrocopy	retro_ogar_197,
Ochotona princeps	ENSOPRG00000011793	2 retrocopies	retro_opri_135, retro_opri_791,
Pongo abelii	ENSPPYG00000017612	2 retrocopies	retro_pabe_2076, retro_pabe_783,
Pan troglodytes	ENSPTRG00000019120	2 retrocopies	retro_ptro_1670, retro_ptro_628,
Rattus norvegicus	ENSRNOG00000049920	2 retrocopies	retro_rnor_2041, retro_rnor_2769,
Sus scrofa	ENSSSCG00000020769	3 retrocopies	retro_sscr_1082, retro_sscr_419, retro_sscr_440,
Ictidomys tridecemlineatus	ENSSTOG00000013334	1 retrocopy	retro_itri_223,
Tarsius syrichta	ENSTSYG00000014299	2 retrocopies	retro_tsyr_132, retro_tsyr_246,
Tursiops truncatus	ENSTTRG00000005649	1 retrocopy	retro_ttru_356,