RetrogeneDB ID:

retro_itri_51

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393305.1:8243706..8245611(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000020232
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSSTOG00000003756
Aliases:None
Description:heat shock 70kDa protein 8 [Source:HGNC Symbol;Acc:5241]


Retrocopy-Parental alignment summary:






>retro_itri_51
ATGTCCGCCCGCGGCCCGGCTATCGGCATCGACCTGGGCACCACCTACTCATGCGTGGGGGTCTTCCAACACGGCAAAGT
GGAAATCATCGCCAATGACCAGGGCAACCGCACCACCCCCAGCTACGTGGCCTTCACGGACACCGAGCGCCTCATCGGCG
ACGCCGCCAAGAACCAAGTGGCCATGAACCCCACTAACACCATCTTCGATGCCAAGAGGCTGATCGGTCGCAAGTTCGAG
GACGCCACGGTGCAGTCGGACATGAAACACTGGCCGTTCCGGGTGGTGAGCGAGGGAGGGAAGCCCAAGGTGCAGGTGGA
GTACAAGGGGGAGATGAAGACCTTCTTCCCCGAGGAGATCTCCTCCATGGTCCTCACTAAGATGAAGGAGATCGCCGAAG
CCTACCTGGGGGGCAAGGTGCAGAGCGCGGTCATCACGGTCCCCGCCTATTTCAACGACTCGCAGCGCCAGGCCACTAAG
GACGCGGGCACTATCACGGGCCTCAACGTGCTGCGCATCATCAACGAGCCCACGGCGGCTGCCATAGCTTACGGCCTGGA
CAAGAAAGGCTGCGCAGGTGGTGAGAAGAACGTGCTCATCTTTGACCTGGGCGGCGGCACCTTCGACGTGTCCATCCTGA
CCATCGAGGATGGCATCTTTGAGGTGAAGTCCACGGCCGGTGACACCCACCTGGGCGGCGAGGACTTCGACAACCGTATG
GTCAGCCACCTGGCAGAAGAGTTCAAGCGCAAGCACAAGAAGGACATTGGGCCCAACAAGCGCGCGGTGCGGCGGCTGCG
CACCGCCTGCGAGCGCGCCAAGCGCACGCTGAGCTCGTCCACACAGGCGAGCATCGAGATCGACTCGCTGTACGAAGGCG
TGGATTTCTACACGTCCATCACCCGCGCCCGCTTCGAGGAGCTCAACGCGGACCTCTTCCGCGGGACCCTGGAGCCGGTG
GAGAAGGCGCTGCGCGACGCCAAACTGGACAAGGGCCAGATCCAGGAGATTGTGCTGGTGGGTGGTTCTACCCGTATCCC
CAAGATCCAGAAGCTGCTGCAAGATTTCTTCAATGGGAAAGAGTTGAACAAGAGCATCAACCCCGACGAGGCGGTGGCCT
ACGGCGCCGCAGTGCAGGCGGCCATCCTCATCGGAGACAAGTCGGAGAACGTGCAGGACCTGCTACTACTAGACGTGACT
CCGTTGTCGTTGGGCATCGAGACGGCTGGCGGCGTCATGACCCCACTCATCAAGAGGAACACCACGATCCCCACCAAGCA
GACGCAGACCTTCACCACCTACTCAGACAACCAGAGCAGCGTGCTGGTGCAAGTGTACGAAGGCGAACGGGCCATGACCA
AGGACAACAACCTGCTAGGCAAGTTCGACCTGACTGGGATTCCCCCAGCACCCCGTGGGGTCCCCCAGATCGAGGTCACC
TTCGACATTGATGCCAACGGCATCCTCAACGTCACCGCTGCTGACAAGAGCACTGGTAAGGAAAACAAAATCACCATTAC
CAACGACAAGGGTCGTCTGAGCAAGGATGACATTGACCGGATGGTTCAAGAGGCGGAGCGGTACAAGTCGGAAGATGAAG
CTAATCGCGACCGGGTCGCAGCCAAAAATGCGGTGGAGTCCTATACCTACAACATCAAGCAGACGGTGGAAGACGAGAAA
CTGAGAGGCAAGATTAGCGAGCAGGACAAAAACAAGATCCTCGACAAGTGTCAGGAGGTGATCAACTGGCTTGACCGAAA
CCAGATGGCAGAAAAAGACGAGTATGAACACAAGCAGAAAGAGCTTGAAAGAGTGTGCAACCCCATCATCAGCAAACTTT
ACCAAGGAGGTCCTGGCGGCGGTTCTGGAGCGTCCGGGGGACCTACTATTGAGGAAGTGGACTAA

ORF - retro_itri_51 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.72 %
Parental protein coverage: 96.44 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAK
..GPA.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNT.FDAK
RetrocopyARGPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTIFDAK
ParentalRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTN
RLIGR.F.DA.VQSDMKHWPF.VV...G.PKVQVEYKGE.K.F.PEE.SSMVLTKMKEIAEAYLG..V..
RetrocopyRLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGEMKTFFPEEISSMVLTKMKEIAEAYLGGKVQS
ParentalAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKK--VGAERNVLIFDLGGGTFDVSI
AV.TVPAYFNDSQRQATKDAGTI.GLNVLRIINEPTAAAIAYGLDKK...G.E.NVLIFDLGGGTFDVSI
RetrocopyAVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGLDKKGCAGGEKNVLIFDLGGGTFDVSI
ParentalLTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQ
LTIEDGIFEVKSTAGDTHLGGEDFDNRMV.H...EFKRKHKKDI..NKRAVRRLRTACERAKRTLSSSTQ
RetrocopyLTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIGPNKRAVRRLRTACERAKRTLSSSTQ
ParentalASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKL
ASIEIDSLYEG.DFYTSITRARFEELNADLFRGTL.PVEKALRDAKLDK.QI..IVLVGGSTRIPKIQKL
RetrocopyASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRDAKLDKGQIQEIVLVGGSTRIPKIQKL
ParentalLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTT
LQDFFNGKELNKSINPDEAVAYGAAVQAAIL.GDKSENVQDLLLLDVTPLSLGIETAGGVMT.LIKRNTT
RetrocopyLQDFFNGKELNKSINPDEAVAYGAAVQAAILIGDKSENVQDLLLLDVTPLSLGIETAGGVMTPLIKRNTT
ParentalIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
IPTKQTQTFTTYSDNQ..VL.QVYEGERAMTKDNNLLGKF.LTGIPPAPRGVPQIEVTFDIDANGILNV.
RetrocopyIPTKQTQTFTTYSDNQSSVLVQVYEGERAMTKDNNLLGKFDLTGIPPAPRGVPQIEVTFDIDANGILNVT
ParentalAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQ
A.DKSTGKENKITITNDKGRLSK.DI.RMVQEAE.YK.EDE..RD.V..KN..ESY..N.K.TVEDEKL.
RetrocopyAADKSTGKENKITITNDKGRLSKDDIDRMVQEAERYKSEDEANRDRVAAKNAVESYTYNIKQTVEDEKLR
ParentalGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGG
GKI...DK.KILDKC.E.INWLD.NQ.AEK.E.EH.QKELE.VCNPII.KLYQ...G...G..GG
RetrocopyGKISEQDKNKILDKCQEVINWLDRNQMAEKDEYEHKQKELERVCNPIISKLYQGGPGGGSGASGG

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_51 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_51 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 23 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Equus caballus ENSECAG000000135102 retrocopies
retro_ecab_291, retro_ecab_628,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Loxodonta africana ENSLAFG000000303124 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 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,
Nomascus leucogenys ENSNLEG000000074198 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,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Ictidomys tridecemlineatus ENSSTOG00000003756 1 retrocopy
retro_itri_51 ,
Ictidomys tridecemlineatus ENSSTOG000000112434 retrocopies
retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,


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