RetrogeneDB ID: retro_ttru_1798

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_92107:8140..9612(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPD1
• Ensembl ID: ENSTTRG00000003417
• Aliases: None
• Description: heat shock 60kDa protein 1 (chaperonin) [Source:HGNC Symbol;Acc:5261]

Sequence

>retro_ttru_1798
ACTGTTGCAAAGTCCATTGACTTAAAAAATAAATATAAAAATGTTGGCGCTAAACGTGTTCAAGATGTTGCCAGTAACAC
AAACGGAGAGGCTGGGGATGACACCACTACTGCTACTGTACTGGCATGCTCTATCTCCAAGGAAGGCTTCGAGAAGGTTA
GCAACGGTGCTAATCCAGTGGAAATCAGGAGAGGTGTGATGTTAGCTGTTGATGCTGTACTTGCTGAACTTAAGAAGCAG
TCTAAACCTGTGACAACCCCGAAAGAGATCGCCCAGATTGCTACGATTTCTGCACATGGAGACAAAGAAATTGGCAACAT
CATTTCTGATGCGATGAAAAAGGTTGGAAGAAAGGGCGTTATCACAGGAAAGGATGGGGAAACACTGAATGATGAACTAG
AAATTATTGAAGGCATGAAGTTTGATAGAGGGTATATCTCTTCATACTTTATTAATATATCAAAAGGTCAGAAATGTGAA
TTCTAAGTTGCCTATGTTCTTTCGAGTGAAAAGAAAATTTCTAGTGTCCAGTCCATTGTTCCTGCTCTTGAAATTGCCAA
CGCTCACCATAAGCCCTGGGTCATAATTGCTGAAGATGTGGATGGAGAAGCTCTAAGTACACTTGTTTTGAATAGGCTGA
AAGTTGGTCTTCAGGCTTTAGCAGTCAAACCTCCAGGTTTTGGTGACAATAGAAAGAATCAGCTTAAAGACATGGCTATT
GCTACTGGCGGTGCAGTATTGGGAGAAGGACTAACTCTAAATCTTGAAGATGTTCAGCCTCATGACTTAGGAAAAGTTGG
AGAGGTCACTGTGACCAAAGGTGATGCCATGCTCTTGAAAGGATAAGGTGACAAGGATCAAATTGAAAAGCATATTCAAG
AAATCCTCGAGCAGTTGGGTATCACAACTAGTGAAAATGGAAAGGAAAAAGTGAATGAACGTCTGGCAAAACTCTCAGAA
GGTGTTGCTGTGCTAAAGTTTGATGGGACAAGTGACTTTGAAGTGAATGAAAAGAAAGACAGAATTACAGATGCCCTTAA
TGCTACCCGAGCTGCTGTTTAAGAAGGCACTGTTTTGGGAGGGGGCTATGTCCTGCTTCGGTGCCTTCCAGCCTTGGATT
CAATAACTCCAGCTAATGAAGATCAAAAAACTGCTATAGAAATTATTTTAAAAACACTCAAAATTCCTGCAATGACCACT
GCTAAGAATGCAGGTATTGAAGGATCACTGATAGTTGAGAACATTTTGCAGAGTTCTTCAGAAGTTGGTTATGATGCTAT
GCTTGGAGATTTTGCGAATATGGTGGAAAAAGGAAATCATTGGTCCAACTAAGGTTGTAAGAACTGCATTACTGGATGCT
GCTGGAGTGGCCTCTCTGTTAACTACAGCAGAAGTTGTAGGTCACAGGAATCCTAAGGAAGAGAACGGATCCCTGGAATG
GGCCAGATGGGTGGATGGGAAGTGCTGTGGGG

Alignment

ORF - retro_ttru_1798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.66 %
• Parental protein coverage: 85.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEIRRGVMLAV
          TVAKSIDLK.KYKN.GAK.VQDVA.NTN.EAGD.TTTATVLA.SI.KEGFEK.S.GANPVEIRRGVMLAV
Retrocopy TVAKSIDLKNKYKNVGAKRVQDVASNTNGEAGDDTTTATVLACSISKEGFEKVSNGANPVEIRRGVMLAV

Parental  DAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGSIISDAMKKVGRKGVITVKDGKTLNDELEIIEGMK
          DAV.AELKKQSKPVTTP.EIAQ.ATISA.GDKEIG.IISDAMKKVGRKGVIT.KDG.TLNDELEIIEGMK
Retrocopy DAVLAELKKQSKPVTTPKEIAQIATISAHGDKEIGNIISDAMKKVGRKGVITGKDGETLNDELEIIEGMK

Parental  FDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVDGEALSTLVL
          FDRGYIS.YFIN.SKGQKCEF..AYVL.SEKKISSVQSIVPALEIANAH.KP.VIIAEDVDGEALSTLVL
Retrocopy FDRGYISSYFINISKGQKCEF*VAYVLSSEKKISSVQSIVPALEIANAHHKPWVIIAEDVDGEALSTLVL

Parental  NRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGEVIVTKDDAMLL
          NRLKVGLQ..AVK.PGFGDNRKNQLKDMAIATGGAV.G.EGLTLNLEDVQPHDLGKVGEV.VTK.DAMLL
Retrocopy NRLKVGLQALAVKPPGFGDNRKNQLKDMAIATGGAVLG-EGLTLNLEDVQPHDLGKVGEVTVTKGDAMLL

Parental  KGKGDKAQIEKRIQEIIEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKDRVTDALNAT
          KG.GDK.QIEK.IQEI.EQL.ITTSE..KEK.NERLAKLS.GVAVLK..GTSD.EVNEKKDR.TDALNAT
Retrocopy KG*GDKDQIEKHIQEILEQLGITTSENGKEKVNERLAKLSEGVAVLKFDGTSDFEVNEKKDRITDALNAT

Parental  RAAVEEGIVLGGGCALLRCLPALDSITPANEDQKIGIEIIKKALKIPAMTIAKNAGVEGSLIVEKILQSS
          RAAV.EG.VLGGG..LLRCLPALDSITPANEDQK..IEII.K.LKIPAMT.AKNAG.EGSLIVE.ILQSS
Retrocopy RAAV*EGTVLGGGYVLLRCLPALDSITPANEDQKTAIEIILKTLKIPAMTTAKNAGIEGSLIVENILQSS

Parental  SEIGYDAMLGDFVNMVEKG-IIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEK-DP-GMGGMGG-M
          SE.GYDAMLGDF.NMVEKG.II.PTKVVRTALLDAAGVASLLTTAEVV....PKEE..DP.GMG.MGG.M
Retrocopy SEVGYDAMLGDFANMVEKG>IIGPTKVVRTALLDAAGVASLLTTAEVVGHRNPKEEN>DP>GMGQMGG<M

Parental  GGGMG
          G...G
Retrocopy GSAVG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1798 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1798 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 16 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013770	1 retrocopy	retro_amel_771,
Bos taurus	ENSBTAG00000012586	1 retrocopy	retro_btau_988,
Canis familiaris	ENSCAFG00000010865	4 retrocopies	retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus	ENSCJAG00000003990	6 retrocopies	retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Dasypus novemcinctus	ENSDNOG00000013226	3 retrocopies	retro_dnov_1990, retro_dnov_2113, retro_dnov_2512,
Echinops telfairi	ENSETEG00000009184	4 retrocopies	retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Loxodonta africana	ENSLAFG00000000053	1 retrocopy	retro_lafr_476,
Macropus eugenii	ENSMEUG00000011987	2 retrocopies	retro_meug_1688, retro_meug_224,
Myotis lucifugus	ENSMLUG00000000871	4 retrocopies	retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta	ENSMMUG00000010489	1 retrocopy	retro_mmul_83,
Monodelphis domestica	ENSMODG00000012289	3 retrocopies	retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furo	ENSMPUG00000007818	3 retrocopies	retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Otolemur garnettii	ENSOGAG00000034053	5 retrocopies	retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Rattus norvegicus	ENSRNOG00000014525	9 retrocopies	retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Tursiops truncatus	ENSTTRG00000003417	3 retrocopies	retro_ttru_1661, retro_ttru_1798 , retro_ttru_951,
Xenopus tropicalis	ENSXETG00000007509	1 retrocopy	retro_xtro_63,