RetrogeneDB ID:

retro_xtro_63

Retrocopy
location
Organism:Xenopus (Xenopus tropicalis)
Coordinates:GL182726.1:8049..9672(-)
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:ENSXETG00000007509
Aliases:None
Description:heat shock 60kDa protein 1 (chaperonin) [Source:Jamboree;Acc:XB-GENE-980059]


Retrocopy-Parental alignment summary:






>retro_xtro_63
GCAAAAGACGTAGTTTTCGGCGGCGAAGCCCGCGCTCGCATGGTGGAAGGCGTGAACATCCTCGCCAACGCGGTGAAAGT
GACTCTGGGCCCCAAGGGCCGCAATGTGGTGCTGGAGCGCTCGTTCGGCGCCCCCACGGTGACCAAGGACGGTGTGTCCG
TGGCCAAGGAGATCGAGCTCAAGGACAAGCTGCAGAACATGGGCGCGCAGCTCGTGAAGGAAGTGGCGTCCAAGACCAGC
GACAACGCCGGTGACGGTACCACCACCGCCACCGTGCTGGCCCAGGCCATTGTGCGCGAAGGCAGCAAGTACGTGGCCGC
CGGTCTGAACCCGATGGATCTGAAGCGCGGCATTGACAAGGCTGTGGCCGCCCTGGTGGAAGAGTTGAAGAAGGCTTCCA
AGCCCACGACGACCTCCAAGGAAATCGCCCAGGTTGGCTCTATTTCTGCCAACTCCGATGAGTCCATCGGCAAAATCATC
GCGGATGCGATGGACAAGGTGGGCAAGGAGGGCGTGATCACCGTGGAAGATGGCAAGAGCCTGAACAACGAGCTCGATGT
CGTGGAAGGCATGCAGTTCGACCGTGGCTATCTGTCGCCCTACTTCATCAACAACCCCGAGAAGCAGGTCGCCCTGCTGG
ACAACCCCTTTGTGCTGCTGTTCGACAAGAAGATCAGCAACATCCGCGATCTGCTGCCGACGCTGGAGGCTGTGGCCAAG
GCAGGCCGTCCGCTGCTGATCATTGCCGAGGAGGTCGAGGGCGAGGCTCTGGCGACCCTGGTGGTGAATACCATCCGCGG
CATCCTGAAGGTGGTGGCTGTGAAGGCGCCTGGCTTCGGCGACCGCCGCAAGGCCATGCTGGAAGACATTGCCATCCTGA
CGGGCGGCAAGGTGATTGCCGAGGAAGTGGGTCTGTCGCTGGAGAAAGTGACCCTGGCCGATCTGGGGCAGGCCAAGCGC
ATCGAAGTGGGCAAGGAGAACACCACCATCATCGATGGCGCAGGCGCTGCTGCTGACATTGAGGCGCGCGTGAAGCAGAT
CCGCATCCAGATCGAGGAGGCCACCAGCGACTACGACCGTGAGAAGCTGCAAGAGCGCGTGGCCAAGCTGGCCGGTGGCG
TGGCCGTGATCAAGGTGGGCGCAGCCACCGAGGTCGAGATGAAGGAAAAGAAGGCCCGCGTGGAAGACGCGCTGCACGCC
ACCCGCGCTGCGGTGGAAGAAGGCATTGTGGCTGGCGGCGGTGTGGCGCTGCTGCGCGCGCGCCAGGCCGTGGGCCAGAT
CAAGAGCGACAACGCCGACCAGGACGCTGGCATCAAGCTGATCTTGAAGGCCATTGAGGCCCCGCTGCGCGAGATCGTCA
ACAACGCTGGCGGCGAAGCCAGCGTGGTGGTGAACGAAGTGCTGAACCGCAAGGGCAACCACGGCTTCAACGCGGCCAAC
GATACCTACGGCGATATGCTGGAAATGGGTATCCTGGATCCGACCAAGGTGACGCGTACCGCGCTGCAAAACGCCGCTTC
CGTGGCCTCGCTGCTGTTGACCACCGAATGCATGGTGGCCGAGGCGCCGAAGGACGAGGCCGCAGCCCCCGCCATGCCCG
ATATGGGCGGCATGGGTGGCATG

ORF - retro_xtro_63 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.14 %
Parental protein coverage: 93.92 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGSPKVTKDGVTVAKAIDLKDKYKNIGAK
AKDV.FG..ARA.M..GV..LA.AV.VT.GPKGR.V..E.S.G.P.VTKDGV.VAK.I.LKDK..N.GA.
RetrocopyAKDVVFGGEARARMVEGVNILANAVKVTLGPKGRNVVLERSFGAPTVTKDGVSVAKEIELKDKLQNMGAQ
ParentalLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEIRRGVMMAVDAVIKELKNQSKPVTTPE
LV..VA..T...AGDGTTTATVLA..I..EG......G.NP....RG...AV.A...ELK..SKP.TT..
RetrocopyLVKEVASKTSDNAGDGTTTATVLAQAIVREGSKYVAAGLNPMDLKRGIDKAVAALVEELKKASKPTTTSK
ParentalEIAQVATISANGDQEIGKIISDAMKRVGRRGVITVKDGKTLHDELEIIEGMKFDRGYISPYFINTAKGQK
EIAQV..ISAN.D..IGKII.DAM..VG..GVITV.DGK.L..EL...EGM.FDRGY.SPYFIN....Q.
RetrocopyEIAQVGSISANSDESIGKIIADAMDKVGKEGVITVEDGKSLNNELDVVEGMQFDRGYLSPYFINNPEKQV
ParentalCEFQDAYLLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVDGEALSTLVLNRLKVGLQVVAVKAPGFG
........LL..KKIS......P.LE.......PL.IIAE.V.GEAL.TLV.N.....L.VVAVKAPGFG
RetrocopyALLDNPFVLLFDKKISNIRDLLPTLEAVAKAGRPLLIIAEEVEGEALATLVVNTIRGILKVVAVKAPGFG
ParentalDNRKNQLKDMAISSGGVVFGEEGLTLNIEDIQPHDFGKVGEVIVTKDDTMLLKGKGDKAQIEKRIQEIHE
D.RK..L.D.AI..GG.V..EE...L..E.....D.G......V.K..T....G.G..A.IE.R...I..
RetrocopyDRRKAMLEDIAILTGGKVIAEE-VGLSLEKVTLADLGQAKRIEVGKENTTIIDGAGAAADIEARVKQIRI
ParentalQLESTNSEYEKEKLNERLAKLSDGVAVIKVGGTSDVEVNEKKDRVTDALNATRAAVEEGIVLGGGCALLR
Q.E...S.Y..EKL.ER.AKL..GVAVIKVG....VE..EKK.RV.DAL.ATRAAVEEGIV.GGG.ALLR
RetrocopyQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGIVAGGGVALLR
ParentalCIPALEALNPANEDQRVGIEIIRRTLKIPAMTIAKNAGVEGSLVVEKIIQSPVEIGYDAMHAEFVNLVEK
...A.......N.DQ..GI..I......P...I..NAG.E.S.VV..........G..A.........E.
RetrocopyARQAVGQIKSDNADQDAGIKLILKAIEAPLREIVNNAGGEASVVVNEVLNRKGNHGFNAANDTYGDMLEM
ParentalGIIDPTKVVRTALMDAAGVASLLTTAEAVVTEIPKEEKDG-GMAGMGGMGGM
GI.DPTKV.RTAL..AA.VASLL.T.E..V.E.PK.E.....M..MGGMGGM
RetrocopyGILDPTKVTRTALQNAASVASLLLTTECMVAEAPKDEAAAPAMPDMGGMGGM

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 24 .72 RPM
SRP007412_heart 0 .00 RPM 38 .23 RPM
SRP007412_kidney 0 .00 RPM 38 .23 RPM
SRP007412_liver 0 .04 RPM 28 .57 RPM
SRP007412_skeletal_muscle 0 .00 RPM 28 .85 RPM

ChIP-Seq - click to see more details

Xenopus tropicalis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_xtro_63 retrocopy.

TSS - click to see more details

Xenopus tropicalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_xtro_63 was not experimentally validated.

Retrocopy orthology:
Xenopus tropicalis 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 25 parental genes, and 94 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,
Choloepus hoffmanni ENSCHOG000000074015 retrocopies
retro_chof_1105, retro_chof_1300, retro_chof_1822, retro_chof_2000, retro_chof_2397,
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,
Homo sapiens ENSG000001443817 retrocopies
retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930, retro_hsap_4018,
Gorilla gorilla ENSGGOG000000082676 retrocopies
retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
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,
Mus musculus ENSMUSG000000259805 retrocopies
retro_mmus_1225, retro_mmus_2494, retro_mmus_3206, retro_mmus_439, retro_mmus_706,
Nomascus leucogenys ENSNLEG000000068747 retrocopies
retro_nleu_1349, retro_nleu_2238, retro_nleu_229, retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii ENSPPYG000000130465 retrocopies
retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848,
Pteropus vampyrus ENSPVAG000000083061 retrocopy
retro_pvam_250,
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,
Ictidomys tridecemlineatus ENSSTOG000000284701 retrocopy
retro_itri_224,
Tarsius syrichta ENSTSYG000000005136 retrocopies
retro_tsyr_1091, retro_tsyr_1181, retro_tsyr_1445, retro_tsyr_2082, retro_tsyr_395, retro_tsyr_804,
Tursiops truncatus ENSTTRG000000034173 retrocopies
retro_ttru_1661, retro_ttru_1798, retro_ttru_951,
Xenopus tropicalis ENSXETG00000007509 1 retrocopy
retro_xtro_63 ,




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