RetrogeneDB ID:

retro_cjac_4100

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:90299613..90300291(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NUDT21
Ensembl ID:ENSCJAG00000012724
Aliases:None
Description:nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:HGNC Symbol;Acc:13870]


Retrocopy-Parental alignment summary:






>retro_cjac_4100
ATGTCTGTGGTACCTCCGAATCACTCACAGACCGGCTGGTCCCCGGGGGTCACTCAGTTAGGCAACAAGTACATCCAGCA
GACCAAGCCCCTCACCCTGGCATGTACCATCAATCTGTACCCTCTTACCAATCATACTTCTGGTACAAAAGAGCCTCTCT
ACAAGAAGGACAGCTCTGTTGCAGCCAGATTTCAGCACATGAGGGAAGAATTTGATTAAATTGGAATGAGGAGGACTGTA
GAAGAGGTTCTGATTGTACACAAGCATCGGTTACCCCATGTGTTACTGCTATAGCTGGGAACAACTTTCTTCAAACTACC
TGGTGGTAAACTTAACCCGGGAGAAGATGAAGTTGAAGGACTGAAATGCTTAATGACAGAGATGCTGCGTCGTCAGGATA
GAGTTCTGCAAGACTGGGTCATTGATGACTGCATTGGTAACTGGTGAATGACTTTTGAACCTCCTCAGTATCCATATATT
CCTGCACATGTTACACAACCTAAGGAACATAAAAAGTTGTTTCTGGTTCAGCTACAAGAAAAAGCTTTGTTTGCAGTCCC
TAAAAATTACAAGCTGGTAGCTGCACCATTGTTTGAATTGTATGACAAAACACCGAGATATGGACCCATCATTTCTAGTC
TCCCTCAGCTGTTGAACACGTTAAATTTTATGCACAAC

ORF - retro_cjac_4100 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.46 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSVVPPNRSQTGWPRGVTQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREE
MSVVPPN.SQTGW..GVTQ.GNKYIQQTKPLTL..TINLYPLTN.T.GTKEPLY.KDSSVAARFQ.MREE
RetrocopyMSVVPPNHSQTGWSPGVTQLGNKYIQQTKPLTLACTINLYPLTNHTSGTKEPLYKKDSSVAARFQHMREE
ParentalFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWV
FD.IGMRRTVE.VLIVH.HRLPHVLLL.LGTTFFKLPGG.LNPGEDEVEGLK.LMTE.L.RQD.VLQDWV
RetrocopyFD*IGMRRTVEEVLIVHKHRLPHVLLL*LGTTFFKLPGGKLNPGEDEVEGLKCLMTEMLRRQDRVLQDWV
ParentalIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGP
IDDCIGNW....FEPPQYPYIPAH.T.PKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYD..P.YGP
RetrocopyIDDCIGNW*M-TFEPPQYPYIPAHVTQPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDKTPRYGP
ParentalIISSLPQLLSRFNFIYN
IISSLPQLL...NF..N
RetrocopyIISSLPQLLNTLNFMHN

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 27 .18 RPM
SRP051959_heart 0 .00 RPM 27 .99 RPM
SRP051959_kidney 0 .00 RPM 31 .79 RPM
SRP051959_liver 0 .00 RPM 25 .36 RPM
SRP051959_lung 0 .00 RPM 28 .81 RPM
SRP051959_lymph_node 0 .00 RPM 30 .09 RPM
SRP051959_skeletal_muscle 0 .00 RPM 21 .55 RPM
SRP051959_spleen 0 .00 RPM 30 .29 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_4100 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_4100 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_4100 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000166281 retrocopy
retro_amel_540,
Bos taurus ENSBTAG000000102072 retrocopies
retro_btau_1655, retro_btau_937,
Callithrix jacchus ENSCJAG00000012724 3 retrocopies
retro_cjac_1121, retro_cjac_2211, retro_cjac_4100 ,
Cavia porcellus ENSCPOG000000037051 retrocopy
retro_cpor_1054,
Equus caballus ENSECAG000000010431 retrocopy
retro_ecab_292,
Erinaceus europaeus ENSEEUG000000034021 retrocopy
retro_eeur_35,
Echinops telfairi ENSETEG000000136341 retrocopy
retro_etel_622,
Felis catus ENSFCAG000000086691 retrocopy
retro_fcat_1843,
Loxodonta africana ENSLAFG000000284651 retrocopy
retro_lafr_610,
Myotis lucifugus ENSMLUG000000049682 retrocopies
retro_mluc_1576, retro_mluc_999,
Macaca mulatta ENSMMUG000000199061 retrocopy
retro_mmul_1360,
Mustela putorius furoENSMPUG000000034511 retrocopy
retro_mputfur_158,
Mus musculus ENSMUSG000000317543 retrocopies
retro_mmus_1949, retro_mmus_1950, retro_mmus_2142,
Nomascus leucogenys ENSNLEG000000019632 retrocopies
retro_nleu_1477, retro_nleu_2493,
Oryctolagus cuniculus ENSOCUG000000172242 retrocopies
retro_ocun_154, retro_ocun_87,
Otolemur garnettii ENSOGAG000000148882 retrocopies
retro_ogar_1450, retro_ogar_630,
Ochotona princeps ENSOPRG000000066891 retrocopy
retro_opri_637,
Pteropus vampyrus ENSPVAG000000145832 retrocopies
retro_pvam_533, retro_pvam_711,
Sorex araneus ENSSARG000000064932 retrocopies
retro_sara_161, retro_sara_580,
Sarcophilus harrisii ENSSHAG000000096511 retrocopy
retro_shar_469,
Sus scrofa ENSSSCG000000298482 retrocopies
retro_sscr_117, retro_sscr_185,
Tupaia belangeri ENSTBEG000000076641 retrocopy
retro_tbel_4003,
Tarsius syrichta ENSTSYG000000146024 retrocopies
retro_tsyr_1685, retro_tsyr_1888, retro_tsyr_790, retro_tsyr_988,
Tursiops truncatus ENSTTRG000000135451 retrocopy
retro_ttru_1087,
Vicugna pacos ENSVPAG000000037012 retrocopies
retro_vpac_340, retro_vpac_605,


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