RetrogeneDB ID:

retro_cjac_1808

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:67082918..67083357(+)
Located in intron of:ENSCJAG00000019193
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000005912
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1808
AACAAATTTCCAAGTACACCCAATAATGTACTGACTGTTTTTGACAACCATGCAGTCACAGTTATGATTGGTGGAGAACC
ATATACTCTCGGACTTTTTGATACTGCAGGGCAAGAGGATTATGACGGATTAGGACCACTGAGTTATTCACAAATAGATG
TATTTCTAGTCTGTTTTTCAGCAGTCTCTCCATCTCCATTTGAAAATGTAAAAGAAAACTGGGTGCCTGAGATAACTCAC
CACTGTCCAAAGACTCCCTTCTTGCTTGTTGGGGCCTACACTGATCTCAGAGATGATCCCTCTACAATTGAGAAACTTGC
CAAGAACAAACAGGATGTCACTCCAGAAACCGCTAAAAAGCTGGCCCATGACCTGAAGGCTGTCAGGTATGTGAAAGTGT
TCTGCACTCACACAGAAAGGCCTGAAGAATGTATTTGAT

ORF - retro_cjac_1808 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.11 %
Parental protein coverage: 75.92 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalNKFPS--EYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENV
NKFPS....V.TVFDN.AVTVMIGGEPYTLGLFDTAGQEDYD.L.PLSY.Q.DVFLVCFS.VSPS.FENV
RetrocopyNKFPSTPNNVLTVFDNHAVTVMIGGEPYTLGLFDTAGQEDYDGLGPLSYSQIDVFLVCFSAVSPSPFENV
ParentalKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYV-ECSALTQ
KE.WVPEITHHCPKTPFLLVG...DLRDDPSTIEKLAKNKQ...TPETA.KLA.DLKAV.YV..CSALTQ
RetrocopyKENWVPEITHHCPKTPFLLVGAYTDLRDDPSTIEKLAKNKQ-DVTPETAKKLAHDLKAVRYV>KCSALTQ
ParentalRGLKNVFD
.GLKNVFD
RetrocopyKGLKNVFD

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 .51 RPM 66 .78 RPM
SRP051959_heart 0 .60 RPM 40 .97 RPM
SRP051959_kidney 0 .67 RPM 45 .24 RPM
SRP051959_liver 0 .28 RPM 34 .98 RPM
SRP051959_lung 1 .01 RPM 68 .11 RPM
SRP051959_lymph_node 1 .00 RPM 80 .73 RPM
SRP051959_skeletal_muscle 0 .46 RPM 27 .52 RPM
SRP051959_spleen 0 .88 RPM 80 .80 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_1808 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1808 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1808 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3404
Gorilla gorilla retro_ggor_2303
Pongo abelii retro_pabe_2801
Parental genes homology:
Parental genes homology involve 31 parental genes, and 127 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000147075 retrocopies
retro_cfam_1587, retro_cfam_1970, retro_cfam_2189, retro_cfam_88, retro_cfam_89,
Choloepus hoffmanni ENSCHOG0000000530610 retrocopies
retro_chof_103, retro_chof_1044, retro_chof_1195, retro_chof_1853, retro_chof_2055, retro_chof_2105, retro_chof_2331, retro_chof_2407, retro_chof_50, retro_chof_800,
Callithrix jacchus ENSCJAG000000006851 retrocopy
retro_cjac_2403,
Callithrix jacchus ENSCJAG000000021444 retrocopies
retro_cjac_1158, retro_cjac_1954, retro_cjac_2917, retro_cjac_847,
Callithrix jacchus ENSCJAG00000005912 6 retrocopies
retro_cjac_1275, retro_cjac_1808 , retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Callithrix jacchus ENSCJAG000000181941 retrocopy
retro_cjac_2687,
Cavia porcellus ENSCPOG000000065434 retrocopies
retro_cpor_1168, retro_cpor_286, retro_cpor_33, retro_cpor_887,
Dipodomys ordii ENSDORG000000103743 retrocopies
retro_dord_17, retro_dord_464, retro_dord_552,
Equus caballus ENSECAG000000191801 retrocopy
retro_ecab_11,
Echinops telfairi ENSETEG000000044431 retrocopy
retro_etel_2010,
Felis catus ENSFCAG000000048534 retrocopies
retro_fcat_129, retro_fcat_1421, retro_fcat_1579, retro_fcat_896,
Homo sapiens ENSG000000708316 retrocopies
retro_hsap_2775, retro_hsap_2968, retro_hsap_3028, retro_hsap_3404, retro_hsap_3848, retro_hsap_4013,
Gorilla gorilla ENSGGOG000000244395 retrocopies
retro_ggor_1932, retro_ggor_2057, retro_ggor_2303, retro_ggor_2593, retro_ggor_2695,
Myotis lucifugus ENSMLUG000000133654 retrocopies
retro_mluc_1076, retro_mluc_1864, retro_mluc_2456, retro_mluc_905,
Macaca mulatta ENSMMUG000000220098 retrocopies
retro_mmul_1449, retro_mmul_1612, retro_mmul_1685, retro_mmul_1900, retro_mmul_1932, retro_mmul_24, retro_mmul_349, retro_mmul_598,
Monodelphis domestica ENSMODG000000160783 retrocopies
retro_mdom_18, retro_mdom_181, retro_mdom_537,
Mustela putorius furoENSMPUG000000159992 retrocopies
retro_mputfur_308, retro_mputfur_957,
Mus musculus ENSMUSG000000066993 retrocopies
retro_mmus_2816, retro_mmus_2995, retro_mmus_3170,
Nomascus leucogenys ENSNLEG000000081984 retrocopies
retro_nleu_2029, retro_nleu_2949, retro_nleu_3007, retro_nleu_679,
Oryctolagus cuniculus ENSOCUG000000099861 retrocopy
retro_ocun_60,
Otolemur garnettii ENSOGAG000000142611 retrocopy
retro_ogar_131,
Ochotona princeps ENSOPRG000000053312 retrocopies
retro_opri_868, retro_opri_995,
Pongo abelii ENSPPYG000000017556 retrocopies
retro_pabe_2240, retro_pabe_2461, retro_pabe_2801, retro_pabe_3215, retro_pabe_3239, retro_pabe_3295,
Rattus norvegicus ENSRNOG000000135361 retrocopy
retro_rnor_2062,
Sorex araneus ENSSARG000000051843 retrocopies
retro_sara_10, retro_sara_220, retro_sara_3,
Sus scrofa ENSSSCG000000035201 retrocopy
retro_sscr_899,
Ictidomys tridecemlineatus ENSSTOG000000008054 retrocopies
retro_itri_1158, retro_itri_1602, retro_itri_1615, retro_itri_431,
Tupaia belangeri ENSTBEG0000000261417 retrocopies
retro_tbel_1091, retro_tbel_1379, retro_tbel_1697, retro_tbel_1711, retro_tbel_183, retro_tbel_2320, retro_tbel_2447, retro_tbel_2721, retro_tbel_4016, retro_tbel_4168, retro_tbel_4184, retro_tbel_4273, retro_tbel_4427, retro_tbel_584, retro_tbel_585, retro_tbel_860, retro_tbel_873,
Tarsius syrichta ENSTSYG0000000067911 retrocopies
retro_tsyr_1575, retro_tsyr_1597, retro_tsyr_1854, retro_tsyr_1976, retro_tsyr_2048, retro_tsyr_2098, retro_tsyr_352, retro_tsyr_387, retro_tsyr_539, retro_tsyr_66, retro_tsyr_963,
Tursiops truncatus ENSTTRG000000057082 retrocopies
retro_ttru_118, retro_ttru_54,
Vicugna pacos ENSVPAG000000069193 retrocopies
retro_vpac_13, retro_vpac_451, retro_vpac_542,


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