RetrogeneDB ID:

retro_cjac_3306

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:9:56182258..56184223(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSCJAG00000007648
Aliases:None
Description:heat shock 70kDa protein 8 [Source:HGNC Symbol;Acc:5241]


Retrocopy-Parental alignment summary:






>retro_cjac_3306
CGGGTCCAGGCCAACACGCCAGCAACCATGTCGAAGGGACCCGCCGTTGGTATTGATCTTGGCACCACCTACTCTTGTGT
GGGTGTTTTCCAGCACGGAAAAGTAGAAATAATTGCCAATGATCAAGGAAACCGAACCACTCCAAGCTATGTCACCTTTA
CGGACACTGAACAATTGATCGGTGATGCCGCAAAGAATCAAGTTGCAATGAACCCCACCAACACGGTTTTTGATGCCAAA
CGTCTGATTGGATGCAGATTTGAAGATGCCATTGTCCAGTCTGATATGAAGCATTGGCCCTTTATGGTAGTGAATGATGC
TGGCAGGCCCAAGGTCCAAGTAGAATACAAGGGAGAGACAAAAAGCTTCTATCCAGAGGAGGTATCCTCTATGGTTCTGA
CAAAGATGAAGGAAATTGCAGAAGCCTACCTTGGGAAGACTGTTACCAATGCTGTGGTCACAGTGCCCGCTTACTTTAAT
GACTCTCAGCGTCAGGCTACCAAAGATGCTGGAACTATTGCTGGTCTCAATGTACTTAGAATTATTAATGAGCCAACTGC
TGCTGCTATTGCTTATGGCTTAGACAAAAAGGTTGGAGCTGAGAGAAACGTGCTGATCTTTGATCTTGGAGGTGGCACTT
TTGATGTGTCAATCCTCACTATTGAGGATGGAATCTTTGAGGTCAAGTCTACAGCTGGAGACACGCACTTGGGTGGAGAA
GATTTTGATAACCGAACGGTCAACCATTTCATTGCTGAGTTCAAGCGCAAGCATAAGAAGGACATAAGTGAGAACAAGAG
AGCTGTAAGACGCCTCTGTACTGCTTGTGAGCGTGCTAAGCGTACTCTCTCTTCTAGCACCCAGGCTAGTATTGAAATCG
ATTCCCTATATAAAGGAATCGACTTCTATACCTCCATTACCCGTGCCTGATTTGAAGAATTGAATGCTGACTTGTTCCGT
GGAACCCTGGACCCCGTAGAGAAGGCCCTTCGAGATGCCAAACTAGACAAGTCTCAAATTCATGATATTGTCCTGGTTGG
TGGTTCTACTCGCATCCCCAAAATTCAGAAGCTTCTCCAAGACTTTTTCAATGGAAAAGAACTGAATAAGAGCATCAACC
CTGATGAAGCTGTTGCTTATGGTGCAGCTGTCCAGGCCGCCATTCTGTCTGGAGATAAGTCTGAAAATGTTCAAGATTTG
CTGCTCTTGGATGTCACTCCTCTTTCCCTTGGCATTGAAACTGCTGGTGGAGTCATGACCATCCTCATCAAGCGTAATAC
TACCATTCCCACCAAGCAGACACAGACCTTCACTACCTATTCCGACAACCAGCCTGGTGTGCTTATTCAGGTTTATGAAG
GTGAGCGTGCCATGACCAAGGATAACAACCTGCTTGGCAAGTTTGAACTTACAGGCATACCTCCTGCACCCCGAGGTGTT
CCTCAGATTGAGGTCACTTTTGACATTGATGCCAATGGCATTCTCAATGTGTCTGCTGTGGACAAGAGTACAGGAAAAGA
GAACAAGATTACTATCACTAATGACAAGGGCTGTTTGAGCAAGGAAGACATTGAACGTATGGTCCAGGGAGCTGAGAAGT
ACAAAGCTGAAGACGAGAAGCAGAGGGACAAAGTGTCATCTAAGAATTCACTTGAATCCTATGCATTTAACATGAAAGCA
ACTGTTGAAGATGAGAAACTTCAAGGCAAGATTAACGATGAGGATAAACAGAAGATTCTGGACAAGTGTAATGAAATTAT
CAACTGGCTTGATAAGAATCAGACTGCCGAGAAGGAAGAATTTGAACATCAGCAAAAAGAGCTGGAGAAAGTCTGCAACC
CCATCATCACCAAGCTGTACCAGAGTGCAGGAGGCATGCCAGGAGGAATGCCTGGAGGATTCCCTGGTGGTGGAGCTCCT
CCCTCTGGTGGTGCTTCCTCAGGGCCCACTATTGAAGAGGTTGAT

ORF - retro_cjac_3306 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.96 %
Parental protein coverage: 99.85 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRQDRNVGSTMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAM
R...N...TMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYV.FTDTE.LIGDAAKNQVAM
RetrocopyRVQANTPATMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVTFTDTEQLIGDAAKNQVAM
ParentalNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIA
NPTNTVFDAKRLIG.RF.DA.VQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIA
RetrocopyNPTNTVFDAKRLIGCRFEDAIVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIA
ParentalEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLG
EAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLG
RetrocopyEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLG
ParentalGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAK
GGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNR.VNHFIAEFKRKHKKDISENKRAVRRL.TACERAK
RetrocopyGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRTVNHFIAEFKRKHKKDISENKRAVRRLCTACERAK
ParentalRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGST
RTLSSSTQASIEIDSLY.GIDFYTSITRA.FEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGST
RetrocopyRTLSSSTQASIEIDSLYKGIDFYTSITRA*FEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGST
ParentalRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMT
RIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMT
RetrocopyRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMT
ParentalVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDID
.LIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDID
RetrocopyILIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDID
ParentalANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKA
ANGILNVSAVDKSTGKENKITITNDKG.LSKEDIERMVQ.AEKYKAEDEKQRDKVSSKNSLESYAFNMKA
RetrocopyANGILNVSAVDKSTGKENKITITNDKGCLSKEDIERMVQGAEKYKAEDEKQRDKVSSKNSLESYAFNMKA
ParentalTVEDEKLQGKINDEDKQKILDKCNEIINWLVKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGM
TVEDEKLQGKINDEDKQKILDKCNEIINWL.KNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGM
RetrocopyTVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGM
ParentalPGGFPGGGAPPSGGASSGPTIEEVD
PGG..............GPTIEEVD
RetrocopyPGGXXXXXXXXXXXXXXGPTIEEVD

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
SRP051959_colon 66 .43 RPM 328 .33 RPM
SRP051959_heart 42 .99 RPM 200 .64 RPM
SRP051959_kidney 67 .29 RPM 314 .33 RPM
SRP051959_liver 96 .15 RPM 456 .22 RPM
SRP051959_lung 69 .59 RPM 320 .55 RPM
SRP051959_lymph_node 88 .47 RPM 414 .60 RPM
SRP051959_skeletal_muscle 47 .67 RPM 227 .20 RPM
SRP051959_spleen 80 .95 RPM 368 .89 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_3306 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3306 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3306 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 29 parental genes, and 88 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,
Callithrix jacchus ENSCJAG000000068801 retrocopy
retro_cjac_2221,
Callithrix jacchus ENSCJAG00000007648 5 retrocopies
retro_cjac_2388, retro_cjac_3306 , retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
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,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Gorilla gorilla ENSGGOG000000083818 retrocopies
retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
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,
Mus musculus ENSMUSG000000156568 retrocopies
retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Oryctolagus cuniculus ENSOCUG000000155334 retrocopies
retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pongo abelii ENSPPYG000000039879 retrocopies
retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
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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