RetrogeneDB ID:

retro_cjac_3181

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:9:11489157..11489644(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000006854
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000016671
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3181
ATGGGGAACATCTTCGCCAACCTCTTCAAGGGCCTTTTTGGCAAAAAGGAAATGCGCATCCGCATGGTGGGCCTGGATGC
TGCGGGGAAAACCAGGATCCTGTACAAGGTCCAGCTGGGCGAGATCGTGACCACCACTCCCACCATAGGCTTCACTGTGG
AAACTTGTGGAGTACAAGAACATCAGCTTCACTGTGTGGGATGTGGGTGGCCAGGACAAGATCCAGCCTCTGTGGCACCA
CTACTTCCAGAACACACAAGGCCTGATCTTCGTGGTGGACAGCAATGACAGAAAGCGCGTGAACGAGGCCCGTGAGGAGC
TCATGAGGATGCTGGCTGAGGACAAGCTCCGGGATGCTGTCCTGGTGTTTGCCAACAAGCAGGACCTCCCCAATGCCATG
AATGTGGCCGAGATCACAGACAAGCTGGGGCTGCAGTCCCTACGCCACAGGAACTGGTACGTTCAAGCCACCAGCGGCGA
AGGGCTC

ORF - retro_cjac_3181 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.62 %
Parental protein coverage: 91.71 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVET-VEYKNISFTVWDVG
MGNIFANLFKGLFGKKEMRI.MVGLDAAGKT.ILYK..LGEIVTT.PTIGF.VET.VEYKNISFTVWDVG
RetrocopyMGNIFANLFKGLFGKKEMRIRMVGLDAAGKTRILYKVQLGEIVTTTPTIGFTVET>VEYKNISFTVWDVG
ParentalGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEI
GQDKI.PLW.HYFQNTQGLIFVVDSNDR.RVNEAREELMRMLAED.LRDAV.LVFANKQDLPNAMN.AEI
RetrocopyGQDKIQPLWHHYFQNTQGLIFVVDSNDRKRVNEAREELMRMLAEDKLRDAV-LVFANKQDLPNAMNVAEI
ParentalTDKLGLHSLRHRNWYIQATCATSGDGL
TDKLGL.SLRHRNWY.QAT...SG.GL
RetrocopyTDKLGLQSLRHRNWYVQAT---SGEGL

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 .09 RPM 78 .14 RPM
SRP051959_heart 0 .12 RPM 53 .20 RPM
SRP051959_kidney 0 .11 RPM 61 .57 RPM
SRP051959_liver 0 .09 RPM 69 .53 RPM
SRP051959_lung 0 .11 RPM 68 .91 RPM
SRP051959_lymph_node 0 .09 RPM 56 .92 RPM
SRP051959_skeletal_muscle 0 .13 RPM 73 .07 RPM
SRP051959_spleen 0 .13 RPM 58 .74 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_3181 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3181 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3181 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 37 parental genes, and 99 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG000000045091 retrocopy
retro_apla_4,
Bos taurus ENSBTAG000000077252 retrocopies
retro_btau_1257, retro_btau_1390,
Callithrix jacchus ENSCJAG000000158422 retrocopies
retro_cjac_1120, retro_cjac_470,
Callithrix jacchus ENSCJAG00000016671 10 retrocopies
retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181 , retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Callithrix jacchus ENSCJAG000000199221 retrocopy
retro_cjac_507,
Cavia porcellus ENSCPOG000000211741 retrocopy
retro_cpor_1310,
Ciona savignyi ENSCSAVG000000070111 retrocopy
retro_csav_2,
Dasypus novemcinctus ENSDNOG000000104543 retrocopies
retro_dnov_2375, retro_dnov_2459, retro_dnov_26,
Dipodomys ordii ENSDORG000000076034 retrocopies
retro_dord_31, retro_dord_351, retro_dord_409, retro_dord_573,
Erinaceus europaeus ENSEEUG000000046384 retrocopies
retro_eeur_328, retro_eeur_660, retro_eeur_684, retro_eeur_76,
Ficedula albicollis ENSFALG000000010881 retrocopy
retro_falb_2,
Felis catus ENSFCAG000000293741 retrocopy
retro_fcat_1829,
Homo sapiens ENSG000001437613 retrocopies
retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus ENSGALG000000053931 retrocopy
retro_ggal_7,
Gorilla gorilla ENSGGOG000000112635 retrocopies
retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae ENSLACG000000190091 retrocopy
retro_lcha_10,
Myotis lucifugus ENSMLUG000000070206 retrocopies
retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta ENSMMUG000000027923 retrocopies
retro_mmul_237, retro_mmul_541, retro_mmul_810,
Mus musculus ENSMUSG000000480761 retrocopy
retro_mmus_1718,
Nomascus leucogenys ENSNLEG000000141373 retrocopies
retro_nleu_210, retro_nleu_227, retro_nleu_2929,
Oryctolagus cuniculus ENSOCUG000000236452 retrocopies
retro_ocun_1137, retro_ocun_247,
Otolemur garnettii ENSOGAG000000109744 retrocopies
retro_ogar_2431, retro_ogar_295, retro_ogar_3353, retro_ogar_974,
Ochotona princeps ENSOPRG000000150632 retrocopies
retro_opri_317, retro_opri_759,
Procavia capensis ENSPCAG000000142022 retrocopies
retro_pcap_15, retro_pcap_23,
Pongo abelii ENSPPYG000000001483 retrocopies
retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pelodiscus sinensis ENSPSIG000000097671 retrocopy
retro_psin_12,
Pan troglodytes ENSPTRG000000020662 retrocopies
retro_ptro_112, retro_ptro_5,
Pteropus vampyrus ENSPVAG000000073831 retrocopy
retro_pvam_1324,
Rattus norvegicus ENSRNOG000000305913 retrocopies
retro_rnor_1268, retro_rnor_1348, retro_rnor_1950,
Sarcophilus harrisii ENSSHAG000000145993 retrocopies
retro_shar_106, retro_shar_462, retro_shar_725,
Sus scrofa ENSSSCG000000139922 retrocopies
retro_sscr_429, retro_sscr_82,
Ictidomys tridecemlineatus ENSSTOG000000092883 retrocopies
retro_itri_1754, retro_itri_273, retro_itri_363,
Tupaia belangeri ENSTBEG000000092189 retrocopies
retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Taeniopygia guttata ENSTGUG000000002331 retrocopy
retro_tgut_2,
Tetraodon nigroviridis ENSTNIG000000116851 retrocopy
retro_tnig_19,
Tursiops truncatus ENSTTRG000000141862 retrocopies
retro_ttru_1679, retro_ttru_347,
Vicugna pacos ENSVPAG000000032244 retrocopies
retro_vpac_281, retro_vpac_328, retro_vpac_6, retro_vpac_78,


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