RetrogeneDB ID:

retro_cpor_610

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_2:46715156..46715834(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000020267
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJB6
Ensembl ID:ENSCPOG00000013953
Aliases:None
Description:DnaJ (Hsp40) homolog, subfamily B, member 6 [Source:HGNC Symbol;Acc:14888]


Retrocopy-Parental alignment summary:






>retro_cpor_610
ATGGTGGATTACTATGAAGTTCTAGGCATGCAGAGACATGTCTCCCCTGAGGACATCAAGAAGGCATACCGGAAACTGGC
ACTACCGTGGCACCCAGATAAAAATCCTGAGAATAAAGAAGAAGCAGAGCAAAAATTCAAACAAGTGGCTGAGGCATATG
AGGTGTTATCAGATGCTAAAAAATGGGACATCTATGACAAATACAGCAAAGAAGGCTTAAATGGTGGTGGAGGAGGTGGA
AGTCATTTTGATAGTCCATTTGAGTTTCCGGAACCCAGACGATGTCTTCAGGGAATTTTTTGGTGGAAGGGAGTCATTTT
CATTCGACTTCTTTGAAGACCCATTTGAAGACATTTTTGGGAACCGAAGGGGTCCCCGAGAGAGAAACCGTGGCACAGGC
TCTTTTTTCTCCGCCTTCAGTGGGTTTCCATCCTTTGGAGGTGGATTTTCTGCATTTGATACAGGATTCACTTCGTTCGG
GTCCCTGGGCCATGGGGGCCTCACTTCATTTTCGTCCACCTCATTTGGCGGCAGTGGCATGGGCAACTTCAAGTCTATAT
CAACTTCTACCAAATCGTGAACGGTAGAAAGATCACCACAAAGAGAATTGTCGAGAATGGTCAAGAAAGAGTAGAAGTTG
AAGAAGATGGACAGTTAAAGTCCTTAACAATAAATGGT

ORF - retro_cpor_610 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.13 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMVDYYEVLGVQRHASPEDIKKAYRKLALQWHPDKNPENKEEAERKFKQVAEAYEVLSDAKKRDIYDKYGK
MVDYYEVLG.QRH.SPEDIKKAYRKLAL.WHPDKNPENKEEAE.KFKQVAEAYEVLSDAKK.DIYDKY.K
RetrocopyMVDYYEVLGMQRHVSPEDIKKAYRKLALPWHPDKNPENKEEAEQKFKQVAEAYEVLSDAKKWDIYDKYSK
ParentalEGLNGGGGGGSHFDSPFEFGF-TFRNPDDVFREFFGGRDPFSFDFFEDPFEDLFGNRRGPRGSRNRGTGS
EGLNGG.GGG....S.F...F..FRNPDDVFREFFGGR..FSFDFFEDPFED.FGNRRGPR..RNRGTGS
RetrocopyEGLNGG-GGGG---SHFDSPF>SFRNPDDVFREFFGGRESFSFDFFEDPFEDIFGNRRGPR-ERNRGTGS
ParentalFFSAFSGFPSFGGGFSAFDTGFTSFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTK-IVNGRKITTKRI
FFSAFSGFPSFGGGFSAFDTGFTSFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTK.IVNGRKITTKRI
RetrocopyFFSAFSGFPSFGGGFSAFDTGFTSFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTK<IVNGRKITTKRI
ParentalVENGQERVEVEEDGQLKSLTING
VENGQERVEVEEDGQLKSLTING
RetrocopyVENGQERVEVEEDGQLKSLTING

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 2 .24 RPM 60 .05 RPM
SRP017611_kidney 1 .57 RPM 46 .80 RPM
SRP017611_liver 1 .00 RPM 32 .38 RPM
SRP040447_lung 1 .59 RPM 52 .84 RPM
SRP040447_skeletal_muscle 1 .42 RPM 39 .10 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_610 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_610 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 26 parental genes, and 121 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000013323 retrocopies
retro_amel_127, retro_amel_685, retro_amel_95,
Bos taurus ENSBTAG000000007713 retrocopies
retro_btau_163, retro_btau_222, retro_btau_248,
Canis familiaris ENSCAFG000000051746 retrocopies
retro_cfam_155, retro_cfam_201, retro_cfam_2085, retro_cfam_2131, retro_cfam_527, retro_cfam_8,
Callithrix jacchus ENSCJAG000000052887 retrocopies
retro_cjac_104, retro_cjac_1455, retro_cjac_1648, retro_cjac_1692, retro_cjac_2922, retro_cjac_3880, retro_cjac_948,
Cavia porcellus ENSCPOG00000013953 17 retrocopies
retro_cpor_1035, retro_cpor_1074, retro_cpor_1147, retro_cpor_1352, retro_cpor_1360, retro_cpor_1364, retro_cpor_259, retro_cpor_325, retro_cpor_38, retro_cpor_40, retro_cpor_538, retro_cpor_610 , retro_cpor_720, retro_cpor_793, retro_cpor_814, retro_cpor_840, retro_cpor_952,
Equus caballus ENSECAG000000090052 retrocopies
retro_ecab_105, retro_ecab_22,
Felis catus ENSFCAG000000156542 retrocopies
retro_fcat_1072, retro_fcat_91,
Homo sapiens ENSG000001059939 retrocopies
retro_hsap_103, retro_hsap_166, retro_hsap_2399, retro_hsap_2400, retro_hsap_4031, retro_hsap_519, retro_hsap_54, retro_hsap_889, retro_hsap_939,
Gorilla gorilla ENSGGOG000000047036 retrocopies
retro_ggor_1819, retro_ggor_201, retro_ggor_210, retro_ggor_251, retro_ggor_478, retro_ggor_719,
Loxodonta africana ENSLAFG000000133844 retrocopies
retro_lafr_105, retro_lafr_107, retro_lafr_260, retro_lafr_468,
Microcebus murinus ENSMICG000000097601 retrocopy
retro_mmur_474,
Myotis lucifugus ENSMLUG000000091234 retrocopies
retro_mluc_1371, retro_mluc_147, retro_mluc_304, retro_mluc_333,
Macaca mulatta ENSMMUG000000031766 retrocopies
retro_mmul_1050, retro_mmul_165, retro_mmul_2326, retro_mmul_243, retro_mmul_379, retro_mmul_970,
Mustela putorius furoENSMPUG000000097974 retrocopies
retro_mputfur_1084, retro_mputfur_11, retro_mputfur_1199, retro_mputfur_70,
Mus musculus ENSMUSG000000291316 retrocopies
retro_mmus_113, retro_mmus_171, retro_mmus_2023, retro_mmus_3273, retro_mmus_435, retro_mmus_870,
Nomascus leucogenys ENSNLEG000000013805 retrocopies
retro_nleu_1524, retro_nleu_2, retro_nleu_2063, retro_nleu_2820, retro_nleu_52,
Oryctolagus cuniculus ENSOCUG000000000642 retrocopies
retro_ocun_240, retro_ocun_83,
Otolemur garnettii ENSOGAG000000106402 retrocopies
retro_ogar_248, retro_ogar_3412,
Pongo abelii ENSPPYG000000182284 retrocopies
retro_pabe_100, retro_pabe_2165, retro_pabe_226, retro_pabe_669,
Pelodiscus sinensis ENSPSIG000000181021 retrocopy
retro_psin_19,
Pteropus vampyrus ENSPVAG000000001551 retrocopy
retro_pvam_24,
Rattus norvegicus ENSRNOG000000103536 retrocopies
retro_rnor_1680, retro_rnor_1930, retro_rnor_212, retro_rnor_2673, retro_rnor_60, retro_rnor_641,
Ictidomys tridecemlineatus ENSSTOG000000029647 retrocopies
retro_itri_1090, retro_itri_1143, retro_itri_169, retro_itri_54, retro_itri_74, retro_itri_832, retro_itri_85,
Tupaia belangeri ENSTBEG000000095867 retrocopies
retro_tbel_1521, retro_tbel_1533, retro_tbel_1571, retro_tbel_1978, retro_tbel_3918, retro_tbel_4142, retro_tbel_67,
Tarsius syrichta ENSTSYG000000054484 retrocopies
retro_tsyr_1358, retro_tsyr_297, retro_tsyr_360, retro_tsyr_491,
Tursiops truncatus ENSTTRG000000139292 retrocopies
retro_ttru_1864, retro_ttru_637,


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