RetrogeneDB ID:

retro_cpor_1072

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_44:2307158..2308128(+)
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:ENSCPOG00000004169
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1072
GATGCTAAGCTTGACAAGTCACAGATTCATGACATTGTCCTGGTGGGTGGTTTTACTTGTATCCCCAAGATCCAGAAGCT
TCCACAAGACTTCTTCAATGGAAAATAATTGAAGAAGAGCATCAACCCTGATGAGGCTGTTGTTTATGGTTCAGCTATCC
AGGCTGCCATCCTATTTGAAGACAAGTCCAAAAACGTTCAAGATTTGCTGTTGTTGGATGTCACTCCTCTTTCTCTTAGT
ATTGAAACTGCTGGTGGAGTCATAACAGTCCTCACTGAGCATAATACTATCATTCCTGTCAAACAGACACAGACCTTTAC
TATCTACTGTGCCAACCAGACTGGTATGCTCATTCAGGTATATGAAAATGAGTGTGCTATGACCAAGAATAACAACATGC
TTGGTAAGTTTGAACTTACAAGCATACCTCCCACCACTTTGTGCTGTTCCTCAGAATGAAGTCATTTTTGATATTGATTC
CAATAGCATCTTCAGTGTCTCTGCAGTGAACAAAACTACAGGCAATGAGAACGAGATTACCATCATTAATGATAAAGGCC
ATTTGAGCAAGGAGGATATAGAGCATATGGCCCAGGAAGCAGAGAAGTATGAAGCTGAGGATGAGAAGCAAAGGGACAAG
GTGTCCTCCAAGAATTCAGTGCAGTCCTGTGCTTTCAATATGAAAGCAACTCTTAAAGATGAGAAAATTCAGGGCAAGAT
CAATGATGAAAATAAACAGAAGTTTCTTGACAAGTGTGATGAAATCATCAACTGGCTGGATAACAATCAGACTGCAGAGA
AGGAAGAATTTGATCAGAAGAAGGTGCTGGAGAAACTCTGCAGTCCCATCGTCACCAAGTTATATCAGAGTGCAGGGGGC
ATGCCTGGAGAAATGCCTGCAGGTTTCCCTGGTGGAAGATCTCCTCCCTCTGGTGGTGCTTCCTCAGGGTCCACCACTGA
AGAGGTTGAT

ORF - retro_cpor_1072 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.15 %
Parental protein coverage: 50.15 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLL
DAKLDKSQIHDIVLVGG.T.IPKIQKL.QDFFNGK.L.KSINPDEAV.YG.A.QAAIL..DKS.NVQDLL
RetrocopyDAKLDKSQIHDIVLVGGFTCIPKIQKLPQDFFNGK*LKKSINPDEAVVYGSAIQAAILFEDKSKNVQDLL
ParentalLLDVTPLSLGIETAGGVMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELT
LLDVTPLSL.IETAGGV.TVL...NT.IP.KQTQTFT.Y..NQ.G.LIQVYE.E.AMTK.NN.LGKFELT
RetrocopyLLDVTPLSLSIETAGGVITVLTEHNTIIPVKQTQTFTIYCANQTGMLIQVYENECAMTKNNNMLGKFELT
ParentalGIPPAPR-GVPQIEVTFDIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEK
.IPP.....VPQ.EV.FDID.N.I..VSAV.K.TG.EN.ITI.NDKG.LSKEDIE.M.QEAEKY.AEDEK
RetrocopySIPPTTL>AVPQNEVIFDIDSNSIFSVSAVNKTTGNENEITIINDKGHLSKEDIEHMAQEAEKYEAEDEK
ParentalQRDKVSSKNSLESYAFNMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEK
QRDKVSSKNS..S.AFNMKAT..DEK.QGKINDE.KQK.LDKC.EIINWLD.NQTAEKEEF..Q.K.LEK
RetrocopyQRDKVSSKNSVQSCAFNMKATLKDEKIQGKINDENKQKFLDKCDEIINWLDNNQTAEKEEFD-QKKVLEK
ParentalVCNPIITKLYQSAGGMPGGMPGGFPGGGAPPSGGASSGPTIEEVD
.C.PI.TKLYQSAGGMPG.MP.GFPGG..PPSGGASSG.T.EEVD
RetrocopyLCSPIVTKLYQSAGGMPGEMPAGFPGGRSPPSGGASSGSTTEEVD

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
SRP017611_brain 0 .00 RPM 1040 .76 RPM
SRP017611_kidney 0 .00 RPM 1326 .39 RPM
SRP017611_liver 0 .00 RPM 602 .54 RPM
SRP040447_lung 0 .00 RPM 1006 .59 RPM
SRP040447_skeletal_muscle 0 .01 RPM 1403 .89 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_1072 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_1072 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus 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 35 parental genes, and 119 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 ENSCJAG000000076485 retrocopies
retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus ENSCPOG00000004169 3 retrocopies
retro_cpor_1072 , retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Dipodomys ordii ENSDORG000000154671 retrocopy
retro_dord_16,
Equus caballus ENSECAG000000135102 retrocopies
retro_ecab_291, retro_ecab_628,
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,
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,
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,
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,
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,
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,
Pan troglodytes ENSPTRG000000044045 retrocopies
retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Ictidomys tridecemlineatus ENSSTOG000000037561 retrocopy
retro_itri_51,
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,


Copyright © RetrogeneDB 2014-2017