RetrogeneDB ID:

retro_cjac_1792

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:55121483..55122060(+)
Located in intron of:ENSCJAG00000007284
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000004909
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1792
ATGTTCAAGGTGGTTCAGAGGACCATGGGGCTGGCCAGCCTGAGCCTACTCACCTTCAAAGTCTCTGCAGCACCGAAAAA
TGACTCCCCTCCCACAAATCCCATGAAGATTTATGAGCTTTTACTCTACTCTGTTCTCAAGGGCCAATCTAAACATGTGG
AGGAGTCAAGGACCCAGCTTGAGAAAAGCATCTCTCAGCTTTGACATTGTCATGAGCGATATACATGTTGGTGTCGGGAA
ACGTACTCCCAAATGAAGCCCAAGATGTAACGTTTGGTTCATTGGGGGTGACACATCTATGAATATCTCCAAAATGCACC
TGCTAGATTTTTTTCCAGGACTGGGTGTTATCGGTTTGGTTGGCCTTGTTGGACTTCTTTTGGCTAGAGCTTCAAAAGTA
AAGAAGCAGGTATTTCTACCTGGTTTCATGAGATTAGTAGCTTCTATCCATTCTCTACAACAACCCGTCAAATTTGTGCA
GGTCAGAAAGGAGAGATTATATGACCCGGGTTTACAAGGATACATAGTCATGGAAGATTTTTGGAAGAAGAACTTTTTAA
AGCCAGGAAATGTAAGG

ORF - retro_cjac_1792 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.84 %
Parental protein coverage: 96.97 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMFKVIQRSVGPASLSLLTFKVYAVPKKDSPPKNSVKVDELSLYSVPKGQSKYVEESRSPLEESISQLRHY
MFKV.QR..G.ASLSLLTFKV.A.PK.DSPP.N..K..EL.LYSV.KGQSK.VEESR..LE.SISQL.H.
RetrocopyMFKVVQRTMGLASLSLLTFKVSAAPKNDSPPTNPMKIYELLLYSVLKGQSKHVEESRTQLEKSISQL*HC
ParentalCEPYTNWCQETYSQTKPKMQSLVQWGLDSYDYLQNAPP-GFFPRLGVIGCAGLIGLFLARGSKMKKLVYP
.E.YT.WC.ETYSQ.KPKM..LV.WG...Y.YLQNAP...FFP.LGVIG..GL.GL.LAR.SK.KK.V..
RetrocopyHERYTCWCRETYSQMKPKM*RLVHWG*HIYEYLQNAPA>DFFPGLGVIGLVGLVGLLLARASKVKKQVFL
ParentalPGFMGLAASLYYPQQAIVFAQVSGERLYDWGLRGYIVIEDLWKENFQKPGNVK
PGFM.L.AS....QQ...F.QV..ERLYD.GL.GYIV.ED.WK.NF.KPGNV.
RetrocopyPGFMRLVASIHSLQQPVKFVQVRKERLYDPGLQGYIVMEDFWKKNFLKPGNVR

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 .02 RPM 6 .32 RPM
SRP051959_heart 0 .05 RPM 7 .84 RPM
SRP051959_kidney 0 .00 RPM 8 .81 RPM
SRP051959_liver 0 .04 RPM 4 .09 RPM
SRP051959_lung 0 .00 RPM 2 .46 RPM
SRP051959_lymph_node 0 .00 RPM 2 .19 RPM
SRP051959_skeletal_muscle 0 .04 RPM 8 .32 RPM
SRP051959_spleen 0 .13 RPM 2 .25 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_1792 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1792 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1792 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_2051
Parental genes homology:
Parental genes homology involve 27 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000127491 retrocopy
retro_amel_1282,
Choloepus hoffmanni ENSCHOG000000002262 retrocopies
retro_chof_2372, retro_chof_839,
Callithrix jacchus ENSCJAG00000004909 8 retrocopies
retro_cjac_1360, retro_cjac_1417, retro_cjac_1448, retro_cjac_1767, retro_cjac_1792 , retro_cjac_1896, retro_cjac_2038, retro_cjac_2063,
Callithrix jacchus ENSCJAG000000082492 retrocopies
retro_cjac_1783, retro_cjac_2464,
Cavia porcellus ENSCPOG000000041971 retrocopy
retro_cpor_309,
Dasypus novemcinctus ENSDNOG000000067101 retrocopy
retro_dnov_2450,
Equus caballus ENSECAG000000134411 retrocopy
retro_ecab_145,
Echinops telfairi ENSETEG000000141503 retrocopies
retro_etel_1052, retro_etel_516, retro_etel_711,
Felis catus ENSFCAG000000000293 retrocopies
retro_fcat_1203, retro_fcat_1657, retro_fcat_1798,
Homo sapiens ENSG000001848315 retrocopies
retro_hsap_1018, retro_hsap_1693, retro_hsap_2670, retro_hsap_3047, retro_hsap_3259,
Gorilla gorilla ENSGGOG000000012004 retrocopies
retro_ggor_1269, retro_ggor_1863, retro_ggor_2098, retro_ggor_806,
Loxodonta africana ENSLAFG000000290701 retrocopy
retro_lafr_1114,
Macropus eugenii ENSMEUG000000142221 retrocopy
retro_meug_700,
Macaca mulatta ENSMMUG000000163614 retrocopies
retro_mmul_1584, retro_mmul_1886, retro_mmul_2051, retro_mmul_814,
Monodelphis domestica ENSMODG000000255541 retrocopy
retro_mdom_1510,
Mustela putorius furoENSMPUG000000001091 retrocopy
retro_mputfur_109,
Mus musculus ENSMUSG000000795081 retrocopy
retro_mmus_282,
Nomascus leucogenys ENSNLEG000000100265 retrocopies
retro_nleu_1167, retro_nleu_1338, retro_nleu_1944, retro_nleu_456, retro_nleu_898,
Otolemur garnettii ENSOGAG000000019606 retrocopies
retro_ogar_1083, retro_ogar_1104, retro_ogar_2092, retro_ogar_2466, retro_ogar_2927, retro_ogar_3094,
Pongo abelii ENSPPYG000000201917 retrocopies
retro_pabe_1394, retro_pabe_1417, retro_pabe_2215, retro_pabe_2417, retro_pabe_2434, retro_pabe_2702, retro_pabe_856,
Pan troglodytes ENSPTRG000000217425 retrocopies
retro_ptro_1147, retro_ptro_1799, retro_ptro_1992, retro_ptro_2205, retro_ptro_746,
Pteropus vampyrus ENSPVAG000000025302 retrocopies
retro_pvam_128, retro_pvam_594,
Rattus norvegicus ENSRNOG000000469184 retrocopies
retro_rnor_1022, retro_rnor_1986, retro_rnor_2096, retro_rnor_2308,
Sarcophilus harrisii ENSSHAG000000087341 retrocopy
retro_shar_125,
Sus scrofa ENSSSCG000000121741 retrocopy
retro_sscr_774,
Tupaia belangeri ENSTBEG000000148886 retrocopies
retro_tbel_1153, retro_tbel_4004, retro_tbel_4261, retro_tbel_4698, retro_tbel_715, retro_tbel_96,
Tarsius syrichta ENSTSYG000000102392 retrocopies
retro_tsyr_1089, retro_tsyr_2155,


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