RetrogeneDB ID:

retro_cjac_2574

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:5:141337975..141338937(+)
Located in intron of:ENSCJAG00000019447
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000002214
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2574
ATGGCGTCGAAGCAGGACCTGAAGCCTAAATTCCAGAAGGGTGAGTGAGTGCTGTGCTTTCATGGGCCTCTTCTGTATGA
AGCAAAGTGTGTAAAGGTTGCCATAAAGGACAAACAAGTGAAATACTTCATACATTACAGTGGTTGGAATAAAAATTGGG
ATGAGTGGGTTCTGGAGAGCCGAGTACTCAAATATGAGGACGCCAATTTGCAGAAACAGTGAGAACTTTAAAAAGCCAAC
CAGGAGCAGTATGCGGAGGGGAAGATGAGAGGGGCTGCCCCAGGACAGAAGTCATCTGGTCTGCAACAGAAAAATGTTGA
CATGAAAACCAAAAAACAAACAGAAAACACCTGGAAATGGAGATGGTGATAGTACCAGTGAGACGACTCAGCCTCCTCGG
AAGAAAAGGGCCCAGGTGGATCCTACTGTTGAAAATGAGGAAACATTCATGAACAGAGTTGAAGTCAAAGTAAAGATTCC
TGAGGAACTAAAACGGTGGCTTGTGGATGACTGTGACTTAATTACCAGGCAAAAGAAGCTCTTTTATCTTCCTGCCAAGA
AGAATGTGGATTCCATTCTTGAGGATTATACAAATTATAAGAAATCTCGTGGAAACACAGATAATAAGGAGTATGCGGTT
AATGAAGTTGTGGCAGGGATAAAAGAATACTTCAGTGTAATGTTGGGACCAGCTACTCTACAAATTTGAGAGACTGCAGT
ATGCTGAAATTCTTGCAGATCACCCTGATGCACCCATGTCCCAGGTGTATGGGGCGCCACATCTGTGATTATTTGTACGA
ATTGGAGCAATGTTGGTCTATACACCTCTGGATGAGAAGAGCCTTGCTTTATTACTGAATTATCTTCACGATTTCCTAAA
GTACCTGGCAAAGAACTCTGCAACTTTGTTTAGTGCCAGTGATTATGAAGTGGTTCCTCCTGAGCACCATCAGAAAGCTG
TG

ORF - retro_cjac_2574 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.82 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 5
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMAPKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDTNL
MA.KQD.KPKFQ.GE.VLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWV.ESRVLKY.D.NL
RetrocopyMASKQDLKPKFQKGE*VLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVLESRVLKYEDANL
ParentalQKQREL-QKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRAR
QKQ.EL..K........G...G............K....K.K.NKQKTPGNGDG.STSET.QPPRKKRA.
RetrocopyQKQ*EL>KKPTRSSMRRGR*EGLPQDRSHLVCNRKMLT*KPK-NKQKTPGNGDGDSTSETTQPPRKKRAQ
ParentalVDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDN
VDPTVENEETFMNRVEVKVKIPEELK.WLVDD.DLITRQK.LFYLPAKKNVDSILEDY.NYKKSRGNTDN
RetrocopyVDPTVENEETFMNRVEVKVKIPEELKRWLVDDCDLITRQKKLFYLPAKKNVDSILEDYTNYKKSRGNTDN
ParentalKEYAVNEVVAGIKEYFNVML-GT-QLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYT
KEYAVNEVVAGIKEYF.VML.GT.QLLYKFER.QYAEILADHPDAPMSQVYGAPHL..LFVRIGAML.YT
RetrocopyKEYAVNEVVAGIKEYFSVML<GT<QLLYKFERLQYAEILADHPDAPMSQVYGAPHL*-LFVRIGAMLVYT
ParentalPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
PLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEV.PPE.H.KAV
RetrocopyPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVVPPEHHQKAV

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 .07 RPM 41 .34 RPM
SRP051959_heart 0 .21 RPM 63 .99 RPM
SRP051959_kidney 0 .24 RPM 72 .19 RPM
SRP051959_liver 0 .11 RPM 40 .90 RPM
SRP051959_lung 0 .24 RPM 58 .89 RPM
SRP051959_lymph_node 0 .27 RPM 43 .58 RPM
SRP051959_skeletal_muscle 0 .13 RPM 34 .22 RPM
SRP051959_spleen 0 .21 RPM 52 .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_2574 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2574 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2574 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 28 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123441 retrocopy
retro_amel_124,
Bos taurus ENSBTAG000000109881 retrocopy
retro_btau_137,
Canis familiaris ENSCAFG000000141131 retrocopy
retro_cfam_20,
Callithrix jacchus ENSCJAG00000002214 5 retrocopies
retro_cjac_2113, retro_cjac_2280, retro_cjac_2574 , retro_cjac_3026, retro_cjac_3179,
Cavia porcellus ENSCPOG000000037783 retrocopies
retro_cpor_114, retro_cpor_1409, retro_cpor_915,
Equus caballus ENSECAG000000080911 retrocopy
retro_ecab_62,
Felis catus ENSFCAG000000121971 retrocopy
retro_fcat_75,
Homo sapiens ENSG000001857873 retrocopies
retro_hsap_309, retro_hsap_3125, retro_hsap_850,
Gorilla gorilla ENSGGOG000000168263 retrocopies
retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana ENSLAFG000000098511 retrocopy
retro_lafr_62,
Myotis lucifugus ENSMLUG000000017561 retrocopy
retro_mluc_324,
Macaca mulatta ENSMMUG000000229261 retrocopy
retro_mmul_1064,
Monodelphis domestica ENSMODG000000115172 retrocopies
retro_mdom_150, retro_mdom_158,
Mustela putorius furoENSMPUG000000154291 retrocopy
retro_mputfur_180,
Mus musculus ENSMUSG000000622709 retrocopies
retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825, retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys ENSNLEG000000086783 retrocopies
retro_nleu_417, retro_nleu_445, retro_nleu_51,
Oryctolagus cuniculus ENSOCUG000000151172 retrocopies
retro_ocun_108, retro_ocun_21,
Otolemur garnettii ENSOGAG000000060474 retrocopies
retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Pongo abelii ENSPPYG000000067034 retrocopies
retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes ENSPTRG000000073513 retrocopies
retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus ENSRNOG000000144106 retrocopies
retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sorex araneus ENSSARG000000045191 retrocopy
retro_sara_15,
Sarcophilus harrisii ENSSHAG000000184021 retrocopy
retro_shar_393,
Sus scrofa ENSSSCG000000017691 retrocopy
retro_sscr_93,
Ictidomys tridecemlineatus ENSSTOG000000132943 retrocopies
retro_itri_111, retro_itri_1545, retro_itri_1608,
Tupaia belangeri ENSTBEG000000018978 retrocopies
retro_tbel_1694, retro_tbel_1704, retro_tbel_4638, retro_tbel_518, retro_tbel_550, retro_tbel_69, retro_tbel_753, retro_tbel_76,
Tursiops truncatus ENSTTRG000000166061 retrocopy
retro_ttru_472,
Vicugna pacos ENSVPAG000000088471 retrocopy
retro_vpac_229,


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