RetrogeneDB ID:

retro_cjac_2700

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:6:22062802..22063461(+)
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:ENSCJAG00000002996
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2700
GCTGCTGACGTGAAGATGAGCAGCTCAGAGGAGGTATCCTGGATTTCCTGGTTCTGAGGGCTCCGTGGCAGTGAATTCTT
CTGTGAAGTGGATGAAGACTACATCCAGGACAAATTTAATCTTACTGGACTCAATGAGCAGGTTCCTCACTATCGACAAG
CTCTAGATATGATCTTGGACCTGGAGTCTGATGAAGAACTGGAAGACAACCCCAGCCAGAGTGACCTGACTGAGCAGGCA
GCCGAGATGCTTTATGGATTGATCCACGCCCGATACATCCTTACCAACCATGGCATCGCCCAGATGTTGGAAAAGTACCG
TCAGGGAGACTTTGGCTATTGTCCCCGTGTGTACTATGAGAAACAGACAGTGCTTCCCATTGGCCTTTCAGACATCCCAG
GTGAAGCCACGGTGAATGTCTACTGCACCAAGTGCATGGATGTGTACACACCCAAGTCATCATGGCACCATCACACGGAT
GGCGCCTATTTCAGCACTGGTTTCTCTCACATGCTCTTCATGGTGCATCCTGAGTACCGGCCCAAACGACCTGCCAACCA
GTTTGTGCCAGGCTGTATGGTTTCAAGATCCATCCGATGGCCTACCAGCTGCAGCTCCAAGCTGCCAGCAACTTCAAGAG
CCCAGTCAAGACGATTCGC

ORF - retro_cjac_2700 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.39 %
Parental protein coverage: 94.42 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSADVKMSSSEEVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDEELEDN
.ADVKMSSSEEVSWISWF.GLRG.EFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLE.DEELEDN
RetrocopyAADVKMSSSEEVSWISWF*GLRGSEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLESDEELEDN
ParentalPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMMLEKYQQGDFGYCPRVYCENQPMLPIG-SDIPGEAMVK
P.QSDL.EQAAEMLYGLIHARYILTN.GIAQ.MLEKY.QGDFGYCPRVY.E.Q..LPIG.SDIPGEA.V.
RetrocopyPSQSDLTEQAAEMLYGLIHARYILTNHGIAQ-MLEKYRQGDFGYCPRVYYEKQTVLPIGLSDIPGEATVN
ParentalLYCPKCMDVYTPKSSQHHHMDDAYFGTGFPHMLFIVHPEYRPKQPANQFVP-RLYGARIHPMAYQLQLQA
.YC.KCMDVYTPKSS.HHH.D.AYF.TGF.HMLF.VHPEYRPK.PANQFVP.RLYG..IHPMAYQLQLQA
RetrocopyVYCTKCMDVYTPKSSWHHHTDGAYFSTGFSHMLFMVHPEYRPKRPANQFVP<RLYGFKIHPMAYQLQLQA
ParentalASNFKSPVKTIR
ASNFKSPVKTIR
RetrocopyASNFKSPVKTIR

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 1 .33 RPM 15 .75 RPM
SRP051959_heart 1 .35 RPM 19 .28 RPM
SRP051959_kidney 1 .49 RPM 23 .25 RPM
SRP051959_liver 1 .75 RPM 20 .92 RPM
SRP051959_lung 1 .40 RPM 19 .34 RPM
SRP051959_lymph_node 1 .42 RPM 19 .25 RPM
SRP051959_skeletal_muscle 2 .23 RPM 29 .39 RPM
SRP051959_spleen 1 .55 RPM 19 .08 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_2700 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2700 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2700 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000057511 retrocopy
retro_acar_107,
Bos taurus ENSBTAG000000088371 retrocopy
retro_btau_885,
Callithrix jacchus ENSCJAG00000002996 1 retrocopy
retro_cjac_2700 ,
Dasypus novemcinctus ENSDNOG000000187281 retrocopy
retro_dnov_697,
Dipodomys ordii ENSDORG000000141791 retrocopy
retro_dord_45,
Erinaceus europaeus ENSEEUG000000064172 retrocopies
retro_eeur_331, retro_eeur_555,
Echinops telfairi ENSETEG000000151683 retrocopies
retro_etel_225, retro_etel_271, retro_etel_769,
Felis catus ENSFCAG000000076422 retrocopies
retro_fcat_1749, retro_fcat_206,
Macropus eugenii ENSMEUG0000000409510 retrocopies
retro_meug_1158, retro_meug_1316, retro_meug_1598, retro_meug_187, retro_meug_1939, retro_meug_40, retro_meug_525, retro_meug_528, retro_meug_751, retro_meug_752,
Monodelphis domestica ENSMODG000000152874 retrocopies
retro_mdom_1433, retro_mdom_1558, retro_mdom_704, retro_mdom_936,
Mustela putorius furoENSMPUG000000111291 retrocopy
retro_mputfur_154,
Oryctolagus cuniculus ENSOCUG000000234832 retrocopies
retro_ocun_1477, retro_ocun_362,
Ochotona princeps ENSOPRG000000121381 retrocopy
retro_opri_970,
Sarcophilus harrisii ENSSHAG000000014782 retrocopies
retro_shar_672, retro_shar_693,
Sus scrofa ENSSSCG000000014141 retrocopy
retro_sscr_538,
Tursiops truncatus ENSTTRG000000141032 retrocopies
retro_ttru_1595, retro_ttru_1740,


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