RetrogeneDB ID: retro_etel_43

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_260944:7846..9772(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000009386
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HSPA8
• Ensembl ID: ENSETEG00000010996
• Aliases: None
• Description: heat shock 70kDa protein 8 [Source:HGNC Symbol;Acc:5241]

Sequence

>retro_etel_43
ATGGCGAAGAGCACGGCCATCGGCATCGACCTGGGCACCACCTACTCGTGCGTGGGCGTGTTCCAGCACGGCAAGGTGGA
GATCATCGCCAACGACCAGGGCAACCGCACCACCCCCAGCTACGTGGCCTTCACCGACACCGAGCGCCTGATCGGCGACG
CGGCCAAGAACCAGGTGGCGCTGAACCCGCAGAACACGGTGTTCGACGCCAAGCGGCTGATCGGCCGCAAGTTCGGCGAT
GCGGTGGTGCAGTCGGACATGAAGCACTGGCCCTTCCAGGTGATCTGCGACGGCGACAAGCCCAAGGTGCAGGTGAGCTA
CAAGGGGGAGACCAAGGCGTTCTACCCCGAGGAGATCTCGTCCATGGTGCTGACCAAGATGAAGGAGATCGCCGAGGCGT
ACCTGGGCCACCCGGTGACCAACGCGGTCATCACGGTGCCCGCCTACTTCAACGACTCGCAGCGCCAGGCCACCAAGGAC
GCGGGCGTGATCGCGGGCCTGAACGTGCTGCGGATCATCAACGAGCCCACGGCGGCGGCCATCGCCTACGGCCTGGACCG
GTCGGGCAAGGGCGAGCGCAACGTGCTCATCTTTGACCTGGGCGGGGGCACGTTCGACGTGTCCATCCTGACCATCGACG
ACGGCATCTTCGAGGTGAAGGCCACGGCCGGCGACACCCACCTGGGCGGGGAGGACTTCGACAACCGGCTGGTGAGCCAC
TTCGTGGAGGAGTTCAAGAGGAAGCACAAGAAGGACATCAGCCAGAACAAGCGCGCCGTCAGGCGGCTGCGCACCGCATG
CGAGAGGGCCAAGCGCACCCTGTCGTCCAGCACCCATGCTAGCCTGGAGATCGACTCCCTGTTCGAGGGCATCGACTTCT
ACACGTCCATCACCAGGGCGCGCTTCGAGGAGCTGTGCTCCGACCTGTTCCGCGGCACCCTGGAGCCCGTGGAGAAGGCC
CTGCGCGACGCCAAGCTGGACAAGGCGCAGGTGCACGACCTGGTGCTGGTGGGGGGCTCCACGCGCATCCCCAAGGTGCA
GAAGCTGCTGCAGGACTTCTTCAACGGGCGCGACCTCAACAAGAGCATCAACCCGGACGAGGCGGTGGCCTATGGGGCGG
CGGTGCAGGCGGCCATCCTGATGGGCGACAAGTCCGAGAACGTGCAGGACCTGCTGCTGCTGGACGTGGCCCCGCTGTCG
CTGGGGCTGGAGACGGCCGGCGGCGTGATGACGGCCCTGATCAAGCGCAACTCCACCATCCCCACCAAGCAGACGCAGAC
CTTCACCACCTACTCGGACAACCAGCCCGGGGTGCTGATCCAGGTGTACGAGGGCGAGAGGGCCATGACGCGGGACAACA
ACCTGCTGGGCCGCTTTGAGCTGAGCGGCATCCCGCCCGCCCCCAGGGGCGTGCCCCAGATCGAGGTGACCTTCGACATC
GACGCCAACGGCATCCTGAACGTCACGGCCACGGACAAGAGCACGGGCAAGGCCAACAAGATCACCATCACCAACGACAA
GGGCCGCCTGAGCAAGGAGGAGATCGAGCGCATGGTGCAGGAGGCCGAGAAGTACAAGGCCGAGGATGAGGTGCAGCGCG
AGAAGGTGTCCGCCAAGAACGCCCTGGAGTCCTACGCCTTCAACATGAAGAGTGCCGTGGAGGACGAGGGGCTCAAGGGC
AAGATCAGCGAGGCCGACAAGAAGAAGGTGCTGGATAAGTGCCAGGAGGTGATCTCCTGGCTCGACGCCAACTCCCTGGC
CGAGAAGGAGGAGTTTGAGCACAAGCGGAAGGAGCTGGAGCAGGTGTGCAACCCCATCATCACTGGCCTCTACCAGGGGG
CAGGGGGCCCCGGGGCCGGGGGCTTTGGGGCTCAGGCTCCCCACGGTGCCTCTGGCTCTGGCCCCACCATTGAGGAAGTG
GATTAG

Alignment

ORF - retro_etel_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.92 %
• Parental protein coverage: 86.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFMDTERLIGDAAKNQVAMNPTNTVFDA
          M.K..A.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAF.DTERLIGDAAKNQVA.NP.NTVFDA
Retrocopy MAKSTAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVALNPQNTVFDA

Parental  KRLIGR-FDDAVVQSDMKHWPFLVVNGAGRPKVQVEYKGETQSFYPEEVSSM-LTKMKEIAEAYLGKTIT
          KRLIGR.F.DAVVQSDMKHWPF.V......PKVQV.YKGET..FYPEE.SSM.LTKMKEIAEAYLG...T
Retrocopy KRLIGRKFGDAVVQSDMKHWPFQVICDGDKPKVQVSYKGETKAFYPEEISSMVLTKMKEIAEAYLGHPVT

Parental  NAVVTVPAYFNDSQRQATKDVETIAGLDVLRIINEPTAAAIACGLDKVG-AERNVLIFDLGGGTFDVSIL
          NAV.TVPAYFNDSQRQATKD...IAGL.VLRIINEPTAAAIA.GLD..G..ERNVLIFDLGGGTFDVSIL
Retrocopy NAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAAIAYGLDRSGKGERNVLIFDLGGGTFDVSIL

Parental  TIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLHTACERAKRTLSSSTQA
          TI.DGIFEVK.TAGDTHLGGEDFDNR.V.HF..EFKRKHKKDIS.NKRAVRRL.TACERAKRTLSSST.A
Retrocopy TIDDGIFEVKATAGDTHLGGEDFDNRLVSHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTHA

Parental  SIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLL
          S.EIDSL.EGIDFYTSITRARFEEL..DLFRGTL.PVEKALRDAKLDK.Q.HD.VLVGGSTRIPK.QKLL
Retrocopy SLEIDSLFEGIDFYTSITRARFEELCSDLFRGTLEPVEKALRDAKLDKAQVHDLVLVGGSTRIPKVQKLL

Parental  QDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTTI
          QDFFNG..LNKSINPDEAVAYGAAVQAAIL.GDKSENVQDLLLLDV.PLSLG.ETAGGVMT.LIKRN.TI
Retrocopy QDFFNGRDLNKSINPDEAVAYGAAVQAAILMGDKSENVQDLLLLDVAPLSLGLETAGGVMTALIKRNSTI

Parental  PTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVSA
          PTKQTQTFTTYSDNQPGVLIQVYEGERAMT.DNNLLG.FEL.GIPPAPRGVPQIEVTFDIDANGILNV.A
Retrocopy PTKQTQTFTTYSDNQPGVLIQVYEGERAMTRDNNLLGRFELSGIPPAPRGVPQIEVTFDIDANGILNVTA

Parental  VDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMK-ATEDEKL
          .DKSTGK.NKITITNDKGRLSKE.IERMVQEAEKYKAEDE.QR.KVS.KN.LESYAFNMK.A.EDE.L
Retrocopy TDKSTGKANKITITNDKGRLSKEEIERMVQEAEKYKAEDEVQREKVSAKNALESYAFNMKSAVEDEGL

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_43 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 35 parental genes, and 119 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004884	2 retrocopies	retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca	ENSAMEG00000008425	1 retrocopy	retro_amel_126,
Anas platyrhynchos	ENSAPLG00000010667	1 retrocopy	retro_apla_6,
Bos taurus	ENSBTAG00000013162	1 retrocopy	retro_btau_354,
Canis familiaris	ENSCAFG00000011666	3 retrocopies	retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis	ENSCING00000009665	1 retrocopy	retro_cint_12,
Callithrix jacchus	ENSCJAG00000007648	5 retrocopies	retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Dipodomys ordii	ENSDORG00000015467	1 retrocopy	retro_dord_16,
Equus caballus	ENSECAG00000013510	2 retrocopies	retro_ecab_291, retro_ecab_628,
Echinops telfairi	ENSETEG00000010996	1 retrocopy	retro_etel_43 ,
Ficedula albicollis	ENSFALG00000005812	1 retrocopy	retro_falb_18,
Felis catus	ENSFCAG00000001132	6 retrocopies	retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens	ENSG00000109971	8 retrocopies	retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
Gorilla gorilla	ENSGGOG00000008381	8 retrocopies	retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Loxodonta africana	ENSLAFG00000030312	4 retrocopies	retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo	ENSMGAG00000001929	1 retrocopy	retro_mgal_9,
Myotis lucifugus	ENSMLUG00000004834	3 retrocopies	retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta	ENSMMUG00000004696	7 retrocopies	retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
Monodelphis domestica	ENSMODG00000012958	2 retrocopies	retro_mdom_127, retro_mdom_99,
Mustela putorius furo	ENSMPUG00000005810	9 retrocopies	retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus	ENSMUSG00000015656	8 retrocopies	retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Nomascus leucogenys	ENSNLEG00000007419	8 retrocopies	retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Oryctolagus cuniculus	ENSOCUG00000015533	4 retrocopies	retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pongo abelii	ENSPPYG00000003987	9 retrocopies	retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Pan troglodytes	ENSPTRG00000004404	5 retrocopies	retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Ictidomys tridecemlineatus	ENSSTOG00000003756	1 retrocopy	retro_itri_51,
Taeniopygia guttata	ENSTGUG00000000491	1 retrocopy	retro_tgut_7,
Takifugu rubripes	ENSTRUG00000005265	1 retrocopy	retro_trub_30,
Tursiops truncatus	ENSTTRG00000011139	6 retrocopies	retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus	ENSXMAG00000001602	1 retrocopy	retro_xmac_20,