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


Retrocopy-Parental alignment summary:






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

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:

ParentalTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEIRRGVMLAV
TVAKSIDLK.KYKN.GAK.VQDVA.NTN.EAGD.TTTATVLA.SI.KEGFEK.S.GANPVEIRRGVMLAV
RetrocopyTVAKSIDLKNKYKNVGAKRVQDVASNTNGEAGDDTTTATVLACSISKEGFEKVSNGANPVEIRRGVMLAV
ParentalDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGSIISDAMKKVGRKGVITVKDGKTLNDELEIIEGMK
DAV.AELKKQSKPVTTP.EIAQ.ATISA.GDKEIG.IISDAMKKVGRKGVIT.KDG.TLNDELEIIEGMK
RetrocopyDAVLAELKKQSKPVTTPKEIAQIATISAHGDKEIGNIISDAMKKVGRKGVITGKDGETLNDELEIIEGMK
ParentalFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVDGEALSTLVL
FDRGYIS.YFIN.SKGQKCEF..AYVL.SEKKISSVQSIVPALEIANAH.KP.VIIAEDVDGEALSTLVL
RetrocopyFDRGYISSYFINISKGQKCEF*VAYVLSSEKKISSVQSIVPALEIANAHHKPWVIIAEDVDGEALSTLVL
ParentalNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGEVIVTKDDAMLL
NRLKVGLQ..AVK.PGFGDNRKNQLKDMAIATGGAV.G.EGLTLNLEDVQPHDLGKVGEV.VTK.DAMLL
RetrocopyNRLKVGLQALAVKPPGFGDNRKNQLKDMAIATGGAVLG-EGLTLNLEDVQPHDLGKVGEVTVTKGDAMLL
ParentalKGKGDKAQIEKRIQEIIEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKDRVTDALNAT
KG.GDK.QIEK.IQEI.EQL.ITTSE..KEK.NERLAKLS.GVAVLK..GTSD.EVNEKKDR.TDALNAT
RetrocopyKG*GDKDQIEKHIQEILEQLGITTSENGKEKVNERLAKLSEGVAVLKFDGTSDFEVNEKKDRITDALNAT
ParentalRAAVEEGIVLGGGCALLRCLPALDSITPANEDQKIGIEIIKKALKIPAMTIAKNAGVEGSLIVEKILQSS
RAAV.EG.VLGGG..LLRCLPALDSITPANEDQK..IEII.K.LKIPAMT.AKNAG.EGSLIVE.ILQSS
RetrocopyRAAV*EGTVLGGGYVLLRCLPALDSITPANEDQKTAIEIILKTLKIPAMTTAKNAGIEGSLIVENILQSS
ParentalSEIGYDAMLGDFVNMVEKG-IIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEK-DP-GMGGMGG-M
SE.GYDAMLGDF.NMVEKG.II.PTKVVRTALLDAAGVASLLTTAEVV....PKEE..DP.GMG.MGG.M
RetrocopySEVGYDAMLGDFANMVEKG>IIGPTKVVRTALLDAAGVASLLTTAEVVGHRNPKEEN>DP>GMGQMGG<M
ParentalGGGMG
G...G
RetrocopyGSAVG

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Tursiops truncatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ttru_1798 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1798 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 16 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Bos taurus ENSBTAG000000125861 retrocopy
retro_btau_988,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Dasypus novemcinctus ENSDNOG000000132263 retrocopies
retro_dnov_1990, retro_dnov_2113, retro_dnov_2512,
Echinops telfairi ENSETEG000000091844 retrocopies
retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Loxodonta africana ENSLAFG000000000531 retrocopy
retro_lafr_476,
Macropus eugenii ENSMEUG000000119872 retrocopies
retro_meug_1688, retro_meug_224,
Myotis lucifugus ENSMLUG000000008714 retrocopies
retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta ENSMMUG000000104891 retrocopy
retro_mmul_83,
Monodelphis domestica ENSMODG000000122893 retrocopies
retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furoENSMPUG000000078183 retrocopies
retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Rattus norvegicus ENSRNOG000000145259 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 ENSXETG000000075091 retrocopy
retro_xtro_63,


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