RetrogeneDB ID:

retro_itri_1879

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH394458.1:13353..14585(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA5
Ensembl ID:ENSSTOG00000011243
Aliases:None
Description:heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) [Source:HGNC Symbol;Acc:5238]


Retrocopy-Parental alignment summary:






>retro_itri_1879
GTCTTCAAATTCATGCCCACCAATAGAGATACTCATCAAGGTGAAGAAGACTTTGACCAGCATGTTATGAAAAATTTCAT
CAGGCTGTACAAAAAGAAGACTGGCAAATATGTTAGGAAAAAAAACAGAGCTGTGCAGAAACTCCAGCATGAAGTAGAAA
AGGCCAAGTGGGCCCTGTCTGCCCAACATTAAGCAAGAATTAAAATTGAGTTCTTCTATGAAGGAGAAGACTTTTCTGAA
ACCCTGACTCAGGCAAAATTTGAAGAGAAAACATGGACCTGTTCTGGTCTACCATGAAACCTGTTCAGAAAGTACTGCAG
GATTCTGACTTGTAGAAGTCTGATATTGATGAGATTGTTCTTGTTGGTGGCTCTAGTCAAATTCCAAATATTCAGCAACT
TGTTAAAGAGTTATTCAATGGCAAGGAACCATTCTGTGGCATAAACCCAGATGAGGCTGTTGCATATGGCGACACTGTCC
AGGCTGGTGTACTCTCTGATGATCCAGATACAGGTGACCTTGCTCTGCTTGATGTATTTCCCCTGACATTTGGTATTGAA
ACTGTGGGAGGTGTCATGACCAAAGTGATACCAAGGAACACAGTGGTACCCACCAAGAGCCTCAGATCTTTTCTCAGCTT
CTGATAAGCAACCTACTGTTCCAATCAATGTCTATGAAGGTAATGGACCCCTGAAAAACGACAACCACCTTCTGGGTACA
TTTGATCTCACTGGAATTCCTCCTGTGGGGTCCCCCAGATTGAAGTCACTTTTGAGATACATATGAATGCTATTCTTTGG
GTTACAGCTGTAGACAAAGGTACAGAGAACAAAAATAAGACTACAATTACTAATGACCAAAATTGCTTGACACTTGAAGA
AATTGAAAAGATGATTAATGATGTTAAGAAGTTTGCTGAGGAAAACAAAAGACTCAAGGAGCATACTGATAGTAGGAATT
AGTTGAAAAGCTATGCCTACTCTATAAAGTATCAAATTGGAGATAAAGAAAAGTTGAGAGGCAAACTTTCCTCTGAAGAT
AAGGAGACCATGGAAAAAGCTGTAGAGGAAAAGACTGAATGGCTGGAAAGCCGCCAAGAAGCTGACATTGAAGACTTCAA
AACTGAAAAGAAGAAACTAAAATAAATTGTTCAGCCAATTAGCAGCAAATTCTATGGAAGTGTAGGCCCTCCCCCAACTG
GTGAAGAGGATAAAGCAGAAAGAGATGAGTTG

ORF - retro_itri_1879 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.51 %
Parental protein coverage: 63.3 %
Number of stop codons detected: 4
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIE
VF....TN.DTH.G.EDFDQ.VM..FI.LYKKKTGK.VR...RAVQKL..EVEKAK.ALS.QH.ARI.IE
RetrocopyVFKFMPTNRDTHQGEEDFDQHVMKNFIRLYKKKTGKYVRXXXRAVQKLQHEVEKAKWALSAQH*ARIKIE
ParentalSFYEGEDFSETLTRAKFEEL-NMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFF
.FYEGEDFSETLT.AKFEE..NMDLF.STMKPVQKVL.DSDL.KSDIDEIVLVGGS..IP.IQQLVKE.F
RetrocopyFFYEGEDFSETLTQAKFEEK<NMDLFWSTMKPVQKVLQDSDL*KSDIDEIVLVGGSSQIPNIQQLVKELF
ParentalNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVVPTK-KS
NGKEP..GINPDEAVAYG..VQAGVLS.D.DTGDL.LLDV.PLT.GIETVGGVMTK.IPRNTVVPTK...
RetrocopyNGKEPFCGINPDEAVAYGDTVQAGVLSDDPDTGDLALLDVFPLTFGIETVGGVMTKVIPRNTVVPTK<EP
ParentalQIFS-TASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVP-QIEVTFEIDVNGILRVTAEDK
QIFS..ASD.QPTV.I.VYEG..PL..DNHLLGTFDLTGIPP...G.P.QIEVTFEI..N.IL.VTA.DK
RetrocopyQIFS<SASDKQPTVPINVYEGNGPLKNDNHLLGTFDLTGIPPV--GSP<QIEVTFEIHMNAILWVTAVDK
ParentalGTGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKRLKERIDTRNELESYAYSLKNQIGDKEKLGGKL
GT.NKNK.TITNDQN.LT.EEIE.M.ND..KFAEE.KRLKE..D.RN.L.SYAYS.K.QIGDKEKL.GKL
RetrocopyGTENKNKTTITNDQNCLTLEEIEKMINDVKKFAEENKRLKEHTDSRN*LKSYAYSIKYQIGDKEKLRGKL
ParentalSSEDKETMEKAVEEKIEWLESHQDADIEDFKAKKKELEEIVQPIISKLYGSAGPPPTGEEDTSERDEL
SSEDKETMEKAVEEK.EWLES.Q.ADIEDFK..KK.L..IVQPI.SK.YGS.GPPPTGEED..ERDEL
RetrocopySSEDKETMEKAVEEKTEWLESRQEADIEDFKTEKKKLK*IVQPISSKFYGSVGPPPTGEEDKAERDEL

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_1879 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1879 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 12 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000068801 retrocopy
retro_cjac_2221,
Homo sapiens ENSG000000445741 retrocopy
retro_hsap_3005,
Gallus gallus ENSGALG000000010001 retrocopy
retro_ggal_21,
Gorilla gorilla ENSGGOG000000268791 retrocopy
retro_ggor_2082,
Macropus eugenii ENSMEUG000000167021 retrocopy
retro_meug_522,
Mus musculus ENSMUSG000000268641 retrocopy
retro_mmus_1299,
Nomascus leucogenys ENSNLEG000000173481 retrocopy
retro_nleu_751,
Otolemur garnettii ENSOGAG000000067861 retrocopy
retro_ogar_2901,
Pongo abelii ENSPPYG000000196091 retrocopy
retro_pabe_2491,
Pan troglodytes ENSPTRG000000005631 retrocopy
retro_ptro_2033,
Ictidomys tridecemlineatus ENSSTOG000000037561 retrocopy
retro_itri_51,
Ictidomys tridecemlineatus ENSSTOG00000011243 4 retrocopies
retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879 ,


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