RetrogeneDB ID:

retro_cjac_1519

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:16:58633785..58634150(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000004328
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000004473
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1519
GAGAAGACCTTCAAGCGGTGCCACACCTTCAAACAAAGAGCAGACAGTGTCCGACTTCTTCGAGAGCAGCATCCATCCAA
ACTCCCGCTGATAGCAGAATGCTTCAAAGGTGAGAAGAAGCTTCCTATCCTGGATAAAATGAAGTCCCTTGTACCTGACC
ATGTCAACATTAGTGAGCTCATCAAGATAATCAAAGGCACGTACAGCTCAATGCTAATCAAGCCTTCTTCCTGTTGGTGA
ATGGACACAGCACGGTGAGCATCTCCACACCAATCTCAGAGGTGTGTGAGAGTGAGAAGGATGAAGATGGATTCCTGTAT
GTGGTTTATTCCTCCCAGGAGATGTTTGGGATGAAATTGTCTGTG

ORF - retro_cjac_1519 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.42 %
Parental protein coverage: 97.6 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIR-RRLQ
EKTFK...TF.QR...VRL.REQHP.K.P.I.E..KGEK.LP.LDK.K.LVPDHVN.SELIKII..R..Q
RetrocopyEKTFKRCHTFKQRADSVRLLREQHPSKLPLIAECFKGEKKLPILDKMKSLVPDHVNISELIKIIK<RHVQ
ParentalLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYASQETFGMKLSV
LNANQAFFLLVNGHS.VS.STPISEV.ESEKDEDGFLY.VY.SQE.FGMKLSV
RetrocopyLNANQAFFLLVNGHSTVSISTPISEVCESEKDEDGFLYVVYSSQEMFGMKLSV

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 4 .66 RPM
SRP051959_heart 0 .00 RPM 10 .24 RPM
SRP051959_kidney 0 .00 RPM 8 .14 RPM
SRP051959_liver 0 .00 RPM 5 .18 RPM
SRP051959_lung 0 .00 RPM 6 .49 RPM
SRP051959_lymph_node 0 .00 RPM 5 .57 RPM
SRP051959_skeletal_muscle 0 .00 RPM 19 .35 RPM
SRP051959_spleen 0 .00 RPM 6 .11 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_1519 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1519 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1519 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 32 parental genes, and 97 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000182542 retrocopies
retro_amel_1660, retro_amel_873,
Bos taurus ENSBTAG000000116321 retrocopy
retro_btau_977,
Canis familiaris ENSCAFG000000199091 retrocopy
retro_cfam_1578,
Choloepus hoffmanni ENSCHOG000000120907 retrocopies
retro_chof_146, retro_chof_2230, retro_chof_2274, retro_chof_2432, retro_chof_510, retro_chof_558, retro_chof_960,
Callithrix jacchus ENSCJAG00000004473 3 retrocopies
retro_cjac_1114, retro_cjac_1519 , retro_cjac_779,
Callithrix jacchus ENSCJAG000000142531 retrocopy
retro_cjac_146,
Callithrix jacchus ENSCJAG000000166552 retrocopies
retro_cjac_2851, retro_cjac_3820,
Cavia porcellus ENSCPOG000000239221 retrocopy
retro_cpor_394,
Dasypus novemcinctus ENSDNOG000000102287 retrocopies
retro_dnov_1008, retro_dnov_1024, retro_dnov_1335, retro_dnov_165, retro_dnov_2435, retro_dnov_2604, retro_dnov_913,
Dipodomys ordii ENSDORG000000138621 retrocopy
retro_dord_376,
Echinops telfairi ENSETEG000000151892 retrocopies
retro_etel_1050, retro_etel_3,
Felis catus ENSFCAG000000019384 retrocopies
retro_fcat_1727, retro_fcat_1874, retro_fcat_340, retro_fcat_884,
Homo sapiens ENSG000001409413 retrocopies
retro_hsap_3695, retro_hsap_487, retro_hsap_62,
Loxodonta africana ENSLAFG000000233643 retrocopies
retro_lafr_1077, retro_lafr_915, retro_lafr_974,
Microcebus murinus ENSMICG000000073562 retrocopies
retro_mmur_117, retro_mmur_507,
Myotis lucifugus ENSMLUG000000155961 retrocopy
retro_mluc_1586,
Macaca mulatta ENSMMUG000000176131 retrocopy
retro_mmul_15,
Mus musculus ENSMUSG000000318124 retrocopies
retro_mmus_1271, retro_mmus_2384, retro_mmus_2619, retro_mmus_846,
Nomascus leucogenys ENSNLEG000000115114 retrocopies
retro_nleu_1032, retro_nleu_1467, retro_nleu_2392, retro_nleu_931,
Oryctolagus cuniculus ENSOCUG000000229704 retrocopies
retro_ocun_1155, retro_ocun_572, retro_ocun_731, retro_ocun_784,
Otolemur garnettii ENSOGAG000000042563 retrocopies
retro_ogar_1468, retro_ogar_2885, retro_ogar_2892,
Ochotona princeps ENSOPRG000000154614 retrocopies
retro_opri_1136, retro_opri_369, retro_opri_85, retro_opri_977,
Pongo abelii ENSPPYG000000076287 retrocopies
retro_pabe_1280, retro_pabe_1566, retro_pabe_245, retro_pabe_3157, retro_pabe_3158, retro_pabe_940, retro_pabe_978,
Pan troglodytes ENSPTRG000000084453 retrocopies
retro_ptro_2505, retro_ptro_367, retro_ptro_63,
Pteropus vampyrus ENSPVAG000000168581 retrocopy
retro_pvam_728,
Rattus norvegicus ENSRNOG000000179055 retrocopies
retro_rnor_1240, retro_rnor_1739, retro_rnor_1865, retro_rnor_1868, retro_rnor_2033,
Sarcophilus harrisii ENSSHAG000000170741 retrocopy
retro_shar_168,
Sus scrofa ENSSSCG000000026552 retrocopies
retro_sscr_188, retro_sscr_737,
Ictidomys tridecemlineatus ENSSTOG000000148262 retrocopies
retro_itri_1505, retro_itri_662,
Tupaia belangeri ENSTBEG0000000116511 retrocopies
retro_tbel_1008, retro_tbel_1644, retro_tbel_2020, retro_tbel_2484, retro_tbel_2561, retro_tbel_3181, retro_tbel_3301, retro_tbel_636, retro_tbel_706, retro_tbel_733, retro_tbel_990,
Tursiops truncatus ENSTTRG000000088212 retrocopies
retro_ttru_1336, retro_ttru_1454,
Vicugna pacos ENSVPAG000000100652 retrocopies
retro_vpac_169, retro_vpac_186,


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