RetrogeneDB ID:

retro_dord_16

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:GeneScaffold_6611:100145..101471(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDORG00000016436
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Hspa8
Ensembl ID:ENSDORG00000015467
Aliases:None
Description:heat shock protein 8 [Source:MGI Symbol;Acc:MGI:105384]


Retrocopy-Parental alignment summary:






>retro_dord_16
GATCTGGGTGGAGGCACCTTTGATGTATCCATCCTGACTATAGACGATGGGATTTTTGAGGTAAAGGCTACAGCTGGGGA
CACCCACTTGGGTGGGGAGGACTTTGATAACAGACTTGTGAGCCACTTTGTGGAGGAATTTAAGAGGAAGCATAAGAAGG
ACATCAGCCAGAACAAGCGGGCTGTGAGGCGGCTGCGCACTGCCTGTGAGAGGGCCAAGAGGACTCTGTCATCCAGCACC
CAGGCCAACCTGGAAATTGACTCACTTTATGAAGGCATTGACTTCTACACATCCATCACTAGGGCTCGTTTTGAAGAGTT
GTGTGCAGATTTGTTTAGGGGTACCCTGGAGCCTGTGGAAAAATCTCTTCGGGATGCCAAGATGGATAAGTCTAAAATCC
ACGATATTGTTTTAGTAGGGGGCTCCACCCGCATCCCGAAGGTACAGAGACTACTTCAGGAGTATTTTAATGGCCGTGAT
CTCAACAAGAGTATCAACCCGGATGAAGCAGTAGCCTATGGAGCTGCAGTCCAGGCAGCTATTTTGATGGGTGACAAGTC
TGAGAAGGTGCAGGATCTGCTTTTGCTGGACGTAGCTCCCCTCTCCCTGGGATTGGAGACAGCTGGGGGTGTGATGACTA
TCTTGATCAAGCGCAACTCCACCATCCCCACTAAACAGACTCAGATCTTCACCACATACTCAGACAACCAGCCTGGGGTA
TTGATCCAGGTATATGAGGGCGAGAGAGCGATGACAAGGGACAACAACCTGTTGGGACGCTTTGACCTGACTGGAATACC
TCCTGCACCCAGGGGAGTTCCTCAGATCGAGGTGACGTTTGACATCGATGCCAATGGTATTCTCAATGTCACAGCCATGG
ACAAGAGCACCGGGAAGGCTAACAAGATCACCATTACCAATGACAAGGGCCGCCTGAGCAAGGAGGAGATTGAACGTATG
GTTCTGGATGCAGAAAAATATAAAGCTGAAGATGAGATCCAAAGGGACAAAATCGCTGCAAAAAATGCCTTAGAATCCTA
TGCTTTCAACATGAAGAGTGCTGTGAGTGACGAAGGTTTGAAGGGAAAGATTAGTGATTCTGATAAAAAGAAAATACTGG
AAAAATGCAATGAGGTCCTTTCCTGGCTGGAAGCCAATCAACTAGCTGAGAAAGATGAATTTGATCATAAGAGAAAGGAA
TTGGAGCAGTTGTGTAACCCCATCATCACAAAACTCTACCAGGGAGGATGCACTGGACCTACCTGTGGGACAGGGTATAC
ACCTGGAAGGGCTGCTTCTGGCCCTACCATTGAAGAAGTAGATTAA

ORF - retro_dord_16 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.32 %
Parental protein coverage: 67.41 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACE
DLGGGTFDVSILTI.DGIFEVK.TAGDTHLGGEDFDNR.V.HF..EFKRKHKKDIS.NKRAVRRLRTACE
RetrocopyDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVSHFVEEFKRKHKKDISQNKRAVRRLRTACE
ParentalRAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVG
RAKRTLSSSTQA..EIDSLYEGIDFYTSITRARFEEL.ADLFRGTL.PVEK.LRDAK.DKS.IHDIVLVG
RetrocopyRAKRTLSSSTQANLEIDSLYEGIDFYTSITRARFEELCADLFRGTLEPVEKSLRDAKMDKSKIHDIVLVG
ParentalGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGG
GSTRIPK.Q.LLQ..FNG..LNKSINPDEAVAYGAAVQAAIL.GDKSE.VQDLLLLDV.PLSLG.ETAGG
RetrocopyGSTRIPKVQRLLQEYFNGRDLNKSINPDEAVAYGAAVQAAILMGDKSEKVQDLLLLDVAPLSLGLETAGG
ParentalVMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMT-DNNLLGKFELTGIPPAPRGVPQIEVTF
VMT.LIKRN.TIPTKQTQ.FTTYSDNQPGVLIQVYEGERAMT.DNNLLG.F.LTGIPPAPRGVPQIEVTF
RetrocopyVMTILIKRNSTIPTKQTQIFTTYSDNQPGVLIQVYEGERAMTRDNNLLGRFDLTGIPPAPRGVPQIEVTF
ParentalDIDANGILNVSAVD---SRKEQITI-HDKGRLAKEDIERMVQEAEKYKAEDEKQRDKV-SKNSLESYAFN
DIDANGILNV.A.D........ITI..DKGRL.KE.IERMV..AEKYKAEDE.QRDK...KN.LESYAFN
RetrocopyDIDANGILNVTAMDKSTGKANKITITNDKGRLSKEEIERMVLDAEKYKAEDEIQRDKIAAKNALESYAFN
ParentalMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMP
MK..V.DE.L.GKI.D.DK.KIL.KCNE...WL..NQ.AEK.EF.H..KELE..CNPIITKLYQ.....P
RetrocopyMKSAVSDEGLKGKISDSDKKKILEKCNEVLSWLEANQLAEKDEFDHKRKELEQLCNPIITKLYQGGCTGP
ParentalGGMPGGFPGGGA
....G..PG..A
RetrocopyTCGTGYTPGRAA

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






RNA-Seq - click to see more details

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Dipodomys ordii was not studied using ChIP-Seq data.

EST - click to see more details

Dipodomys ordii was not studied using EST data.

TSS - click to see more details

Dipodomys ordii was not studied using FANTOM5 data.

Lab - click to see more details

retro_dord_16 was not experimentally validated.

Retrocopy orthology:
Dipodomys ordii 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 27 parental genes, and 74 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
retro_amel_126,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Bos taurus ENSBTAG000000131621 retrocopy
retro_btau_354,
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,
Dipodomys ordii ENSDORG00000015467 1 retrocopy
retro_dord_16 ,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Felis catus ENSFCAG000000011326 retrocopies
retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens ENSG000001099718 retrocopies
retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
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,
Macaca mulatta ENSMMUG000000046967 retrocopies
retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
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,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Pan troglodytes ENSPTRG000000044045 retrocopies
retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Tursiops truncatus ENSTTRG000000111396 retrocopies
retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,




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