RetrogeneDB ID:

retro_cjac_3417

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01178854.1:4777..5783(+)
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:ENSCJAG00000012525
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3417
ATGGCTGCTGAAGGTGATTTATTGCTGCTGCAGCTCCCCAAGCTGCTTAAAACCAGCAAACAGCTTCTGGAAATAGAAGA
AGTAGTGACTGAATCTGCCGGTTTCCGGATAGTCCAGGAGAAGATGTTCAAGGACCTGGACCTCCTTGAGAAGGCTGCCA
AAATGTTGTCGCAGCTCGACTTATTCAGTCAAAATGAAGATTTGGAAGAGATTGCTTCCACTGACCTGAAGTACCTATTT
GGTGCTAGCATTTCAAGGAGCCCTCACCATAAAATAAGTCAACCCCAGCAAATGTCTAGATCCTTTGCAGTGGGCTTGAG
AACACTTTATAAACTACTTAACTAAGTGCCATTGCTATCATGTGGCAAAGTCTGAGCTGCCCAAAGCCAAGAACTCTGCT
GAAAATCACACTGCTAATTCCTCTATGGCTTATCCTCGCCTCATTGCTATGGCAGCTCAAAGACAGATTAAAATAGAGAG
ATACAAGCAGAAGAAGGATTTGGAGCATAGGTTGTCTGCAATGAAATCTGCTGTGGAAAGTGGTCAAGCAGATGACGAGC
ATGTTCATGAATCTTATCTTCACCTTCCGAGGTGGATAGATATCAGCTTAGAAGAGATTGAGAGCATTGACCAGGAAATA
AAGTTTCCTGAGAGAAAGAAATGCTTCAAGAGAGGAATCAACTTCTAACTTATCTTGCAGGAGAGGCCTCCAGTGAAACC
CTTCATTCTCACTTGGAACATGGCCCAAGTCTAATTATCTGGAGCTGGTTATTCAAACCTGGCAACTATGATGGTGAGTG
ACTGGTATGAGCAACGTTAGAAATATGGAGCATTCCCAGATCAGGGAGTGATCAAGGCAACACCAGAGGAATTAAGAAAA
GCAGCTCAGCAACAGGAAGATTAAGAAGAAAAAGAGGAGGAGGATGAACAAACACTGTACGGAGCTCAGGAGTGGGATGA
CTGGAAAAGCACCCATCTGAGGGGCTATGGTGACCGACACAACATG

ORF - retro_cjac_3417 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.66 %
Parental protein coverage: 99.71 %
Number of stop codons detected: 5
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMAAEDELLLPRLPELFESSKQLLDEVEVATEPAGSRIVQEKVFKGLDLLEKAAEMLKQLDLFSRNEDLEE
MAAE..LLL..LP.L...SKQLL...EV.TE.AG.RIVQEK.FK.LDLLEKAA.ML.QLDLFS.NEDLEE
RetrocopyMAAEGDLLLLQLPKLLKTSKQLLEIEEVVTESAGFRIVQEKMFKDLDLLEKAAKMLSQLDLFSQNEDLEE
ParentalIASTDLKYL-LVPAFQGALTMKQVNPSKRLDHLQQAREHFINYLTECRCHHVAEFELPKTKDNSAENHTA
IASTDLKYL.LV.AFQGALT.K.VNPSK.LD.LQ.A.EHFINYLT.C.C.HVA..ELPK.K.NSAENHTA
RetrocopyIASTDLKYL>LVLAFQGALTIK*VNPSKCLDPLQWA*EHFINYLTKCHCYHVAKSELPKAK-NSAENHTA
ParentalNSSMAYPSLVAMASQRQAKIERYKQKKELEHRLSTMKSAVESGQADDERVREYYLLHLQRWIDISLEEIE
NSSMAYP.L.AMA.QRQ.KIERYKQKK.LEHRLS.MKSAVESGQADDE.V.E.YL.HL.RWIDISLEEIE
RetrocopyNSSMAYPRLIAMAAQRQIKIERYKQKKDLEHRLSAMKSAVESGQADDEHVHESYL-HLPRWIDISLEEIE
ParentalSIDQEIK-ILRERGSSREASTSNAS-RLERPPMKPFILTRNTAQAKVFGAGYPSLATMTVSDWYEQHRKH
SIDQEIK..LRER..SRE.STSN.S...ERPP.KPFILT.N.AQ....GAGY..LATM.VSDWYEQ..K.
RetrocopySIDQEIK>FLRERNASREESTSNLS<LQERPPVKPFILTWNMAQV*LSGAGYSNLATMMVSDWYEQR*KY
ParentalGALPDQGIAKETPEEFRKAAQQQENQEKKEEDDDEQTLYRAREWDDWKDTHPRGYGNRQNM
GA.PDQG..K.TPEE.RKAAQQQE..E.KEE..DEQTLY.A.EWDDWK.TH.RGYG.R.NM
RetrocopyGAFPDQGVIKATPEELRKAAQQQED*EEKEE-EDEQTLYGAQEWDDWKSTHLRGYGDRHNM

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 8 .25 RPM
SRP051959_heart 0 .00 RPM 11 .02 RPM
SRP051959_kidney 0 .00 RPM 12 .87 RPM
SRP051959_liver 0 .00 RPM 10 .38 RPM
SRP051959_lung 0 .00 RPM 11 .39 RPM
SRP051959_lymph_node 0 .00 RPM 10 .09 RPM
SRP051959_skeletal_muscle 0 .00 RPM 11 .71 RPM
SRP051959_spleen 0 .00 RPM 12 .92 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_3417 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3417 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3417 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000077971 retrocopy
retro_btau_215,
Choloepus hoffmanni ENSCHOG000000136543 retrocopies
retro_chof_1523, retro_chof_2206, retro_chof_438,
Callithrix jacchus ENSCJAG00000012525 6 retrocopies
retro_cjac_111, retro_cjac_1225, retro_cjac_2278, retro_cjac_2968, retro_cjac_3417 , retro_cjac_47,
Cavia porcellus ENSCPOG000000107971 retrocopy
retro_cpor_44,
Dasypus novemcinctus ENSDNOG000000147315 retrocopies
retro_dnov_1160, retro_dnov_2029, retro_dnov_2340, retro_dnov_2380, retro_dnov_678,
Echinops telfairi ENSETEG000000033971 retrocopy
retro_etel_1637,
Felis catus ENSFCAG000000296881 retrocopy
retro_fcat_23,
Homo sapiens ENSG000000892895 retrocopies
retro_hsap_1317, retro_hsap_1848, retro_hsap_2766, retro_hsap_2919, retro_hsap_3059,
Gorilla gorilla ENSGGOG000000277952 retrocopies
retro_ggor_112, retro_ggor_2020,
Myotis lucifugus ENSMLUG000000041791 retrocopy
retro_mluc_316,
Macaca mulatta ENSMMUG000000139292 retrocopies
retro_mmul_1545, retro_mmul_31,
Mus musculus ENSMUSG000000312211 retrocopy
retro_mmus_169,
Nomascus leucogenys ENSNLEG000000007475 retrocopies
retro_nleu_1399, retro_nleu_1653, retro_nleu_2334, retro_nleu_671, retro_nleu_828,
Otolemur garnettii ENSOGAG000000117971 retrocopy
retro_ogar_110,
Pongo abelii ENSPPYG000000204354 retrocopies
retro_pabe_1099, retro_pabe_1451, retro_pabe_2245, retro_pabe_2533,
Pan troglodytes ENSPTRG000000219905 retrocopies
retro_ptro_1233, retro_ptro_1873, retro_ptro_1973, retro_ptro_1982, retro_ptro_901,
Pteropus vampyrus ENSPVAG000000054831 retrocopy
retro_pvam_1462,
Rattus norvegicus ENSRNOG000000262671 retrocopy
retro_rnor_311,
Tarsius syrichta ENSTSYG000000062142 retrocopies
retro_tsyr_1537, retro_tsyr_2131,


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