RetrogeneDB ID:

retro_cjac_625

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:145337837..145338310(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000012116
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_625
GAAGAGAGCTTCATACATTCCTTCTCCTCTGCCTCTGATGCAGAACTTGGTGCTGTGGTTGAATATTCAGAGGATATTAT
CAAGGATGATGAATTCCAGGTATTATAGAGAAATTTCATGGGCAAATACTACCAGGAGTTTGAAGACAAGGAAAAGAATT
AACTCAGCTATATTGCATGTTTTTAGTGAATAAATTTATTTGGTGGAAAAGTATATTAAAAGACAGCTTCTGGAGCAGAT
TCCTCGGTTTAACATGGCAGCTTTTACAACAACGTTACAGCACAGTAAAGATGAAATGGCTGGTGACATATTCAACATGC
TGCTCCCATTTATGGATTTTCTAGCTTTTAAATAAATGTTTTTGAATACAGAGCAGCAAAAGGCAGCCAGGGATAGGACT
TACATTATGGTTTAGTGGTGACTTGTTGTGCAAATTATCCTCTAGGCCAGCTTCCTGAAACCACCTATAGCAC

ORF - retro_cjac_625 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.7 %
Parental protein coverage: 97.53 %
Number of stop codons detected: 7
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalEESFALSFSSASDAEFDAVVGYLEDIIMDDKFQLLQRNFMDKYYLEFEDTEENKLTYTP-IFNEYISLVE
EESF..SFSSASDAE..AVV.Y.EDII.DD.FQ.L.RNFM.KYY.EFED.E.N.L.Y....F.E.I.LVE
RetrocopyEESFIHSFSSASDAELGAVVEYSEDIIKDDEFQVL*RNFMGKYYQEFEDKEKN*LSYIA>VFSE*IYLVE
ParentalKYVEEQLLERIPGFNMAAFTVTLQHHRDEVAGDIFDMLLTFTDFLAFKEMFL-DYRAEKEGRGLDLSSGL
KY...QLLE.IP.FNMAAFT.TLQH..DE.AGDIF.MLL.F.DFLAFK.MFL..YRA.K...G.DL..GL
RetrocopyKYIKRQLLEQIPRFNMAAFTTTLQHSKDEMAGDIFNMLLPFMDFLAFK*MFL<EYRAAKGSQG*DLHYGL
ParentalVVTS-LCKSSSVPASPNNLRH
VVT..LCK.SS.PAS.N.L.H
RetrocopyVVTC<LCKLSSRPAS*NHL*H

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 0 .00 RPM 5 .59 RPM
SRP051959_heart 0 .00 RPM 8 .37 RPM
SRP051959_kidney 0 .00 RPM 8 .39 RPM
SRP051959_liver 0 .00 RPM 1 .86 RPM
SRP051959_lung 0 .00 RPM 11 .22 RPM
SRP051959_lymph_node 0 .00 RPM 6 .89 RPM
SRP051959_skeletal_muscle 0 .00 RPM 4 .45 RPM
SRP051959_spleen 0 .00 RPM 5 .86 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_625 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_625 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_625 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4293
Pan troglodytes retro_ptro_2910
Gorilla gorilla retro_ggor_2868
Parental genes homology:
Parental genes homology involve 31 parental genes, and 133 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000048441 retrocopy
retro_btau_362,
Canis familiaris ENSCAFG000000087853 retrocopies
retro_cfam_1026, retro_cfam_1235, retro_cfam_1357,
Choloepus hoffmanni ENSCHOG0000000901616 retrocopies
retro_chof_1180, retro_chof_1220, retro_chof_1287, retro_chof_1526, retro_chof_1655, retro_chof_1677, retro_chof_1858, retro_chof_1904, retro_chof_2024, retro_chof_2189, retro_chof_2247, retro_chof_2646, retro_chof_2658, retro_chof_408, retro_chof_500, retro_chof_977,
Callithrix jacchus ENSCJAG00000012116 9 retrocopies
retro_cjac_1766, retro_cjac_1920, retro_cjac_1928, retro_cjac_2548, retro_cjac_2580, retro_cjac_2698, retro_cjac_4074, retro_cjac_625 , retro_cjac_689,
Cavia porcellus ENSCPOG000000114065 retrocopies
retro_cpor_1501, retro_cpor_203, retro_cpor_249, retro_cpor_299, retro_cpor_571,
Dipodomys ordii ENSDORG000000163422 retrocopies
retro_dord_227, retro_dord_579,
Equus caballus ENSECAG000000166213 retrocopies
retro_ecab_307, retro_ecab_344, retro_ecab_754,
Felis catus ENSFCAG000000029373 retrocopies
retro_fcat_400, retro_fcat_69, retro_fcat_974,
Homo sapiens ENSG000001029317 retrocopies
retro_hsap_1189, retro_hsap_1846, retro_hsap_3237, retro_hsap_3263, retro_hsap_3270, retro_hsap_4293, retro_hsap_999,
Gorilla gorilla ENSGGOG000000054715 retrocopies
retro_ggor_2159, retro_ggor_2202, retro_ggor_2222, retro_ggor_2868, retro_ggor_927,
Loxodonta africana ENSLAFG000000086333 retrocopies
retro_lafr_103, retro_lafr_228, retro_lafr_418,
Microcebus murinus ENSMICG000000124676 retrocopies
retro_mmur_1066, retro_mmur_1385, retro_mmur_1444, retro_mmur_1515, retro_mmur_247, retro_mmur_499,
Myotis lucifugus ENSMLUG000000126803 retrocopies
retro_mluc_1338, retro_mluc_1843, retro_mluc_746,
Macaca mulatta ENSMMUG000000203527 retrocopies
retro_mmul_1260, retro_mmul_2037, retro_mmul_2055, retro_mmul_2059, retro_mmul_223, retro_mmul_2232, retro_mmul_2458,
Monodelphis domestica ENSMODG000000135111 retrocopy
retro_mdom_1182,
Mustela putorius furoENSMPUG000000043062 retrocopies
retro_mputfur_1046, retro_mputfur_1369,
Nomascus leucogenys ENSNLEG000000028037 retrocopies
retro_nleu_1050, retro_nleu_1939, retro_nleu_1946, retro_nleu_2114, retro_nleu_2332, retro_nleu_2428, retro_nleu_955,
Oryctolagus cuniculus ENSOCUG000000005821 retrocopy
retro_ocun_431,
Otolemur garnettii ENSOGAG000000145359 retrocopies
retro_ogar_1448, retro_ogar_1476, retro_ogar_1657, retro_ogar_1658, retro_ogar_1919, retro_ogar_2427, retro_ogar_2475, retro_ogar_3184, retro_ogar_3352,
Ochotona princeps ENSOPRG000000069312 retrocopies
retro_opri_675, retro_opri_98,
Procavia capensis ENSPCAG000000056642 retrocopies
retro_pcap_110, retro_pcap_84,
Pongo abelii ENSPPYG000000073848 retrocopies
retro_pabe_1318, retro_pabe_1348, retro_pabe_1453, retro_pabe_2684, retro_pabe_2704, retro_pabe_3498, retro_pabe_843, retro_pabe_990,
Pan troglodytes ENSPTRG000000081507 retrocopies
retro_ptro_1231, retro_ptro_2189, retro_ptro_2207, retro_ptro_2910, retro_ptro_2948, retro_ptro_752, retro_ptro_816,
Pteropus vampyrus ENSPVAG000000013912 retrocopies
retro_pvam_507, retro_pvam_788,
Rattus norvegicus ENSRNOG000000169911 retrocopy
retro_rnor_780,
Sorex araneus ENSSARG000000054421 retrocopy
retro_sara_190,
Ictidomys tridecemlineatus ENSSTOG000000102541 retrocopy
retro_itri_638,
Tupaia belangeri ENSTBEG000000144411 retrocopy
retro_tbel_2991,
Tarsius syrichta ENSTSYG0000000492310 retrocopies
retro_tsyr_1003, retro_tsyr_1066, retro_tsyr_1205, retro_tsyr_1728, retro_tsyr_1755, retro_tsyr_1958, retro_tsyr_2144, retro_tsyr_28, retro_tsyr_298, retro_tsyr_351,
Tursiops truncatus ENSTTRG000000127943 retrocopies
retro_ttru_1403, retro_ttru_325, retro_ttru_973,
Vicugna pacos ENSVPAG000000059762 retrocopies
retro_vpac_242, retro_vpac_554,


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