RetrogeneDB ID:

retro_cjac_1769

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:34708210..34708942(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000006127
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000015844
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1769
GTGGATAAAAATGAGCTGGTTCATAGGGCCAAACTGGCCAAGCAGGCTGAGAGAGATGACATGGCAGCCTGCACGAAGTC
TATAACTAAGCAAGTAGCTGCATTATCCAATGAAGAGAGGAATCTCTTCCCAGTTGCTTATAAAAATGTTGTAGGAGCCC
GTAGGTCATCTTGGAGGGTCGTCTCAAGTATTGAACAAAAGACAGAAAGTTCTGAGAAAAAAACAGCAGATGGCTTGAGA
ATACAGAGAGAAAATTGGAAAGGAACTAAGAGATACCTGCAATGATGTACTGTCTCTTTTGGAAAAGTTCTTGATACCCA
ATGCTTCACAAGCAGAGAGCAAAGTCTTCTATTTGAAAATGGAAGGAGAATACCACTATTACTTGGCTGAGGTTGCCGCT
GGTGAAGACAAGAAAGGGATTGTGGATGAGTCACAACAAGCATACCAAGAAGCTTTTGAAATCAGCAAAAAGCAAATGCA
ATCAACAAATCCTATCAGACTGGGTCTGGCCCTTAACTTCTCTAGTTCTATTTTGAGATTCTGAACTCCCCAGAGAAAGC
CTGCTCTCTTGCAAAGACAGCTTTTGATGAAGCTATTGCTGAACTTGATACATTAAGTGAGGAGTCATACAAAGACAGCA
CGCTAATAATGCAATTACTGAGAGACAACTTGACATTGTGGACATCGGATACCCAAGGAGAGGAAGCTGAAGCAGGAGAA
GGAGGGGGAAAT

ORF - retro_cjac_1769 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.64 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTE
.DKNELV..AKLA.QAER.DDMAAC.KS.T.Q.A.LSNEERNL..VAYKNVVGARRSSWRVVSSIEQKTE
RetrocopyVDKNELVHRAKLAKQAER-DDMAACTKSITKQVAALSNEERNLFPVAYKNVVGARRSSWRVVSSIEQKTE
ParentalGAEKK-QQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKK
..EKK.QQMA.EYREKI..ELRD.CNDVLSLLEKFLIPNASQAESKVFYLKM.G.Y..YLAEVAAG.DKK
RetrocopySSEKK>QQMA*EYREKIGKELRDTCNDVLSLLEKFLIPNASQAESKVFYLKMEGEYHYYLAEVAAGEDKK
ParentalGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSV-FYYEILNSPEKACSLAKTAFDEAIAELDTLSE
GIVD.SQQAYQEAFEISKK.MQ.T.PIRLGLALNFS..FY.EILNSPEKACSLAKTAFDEAIAELDTLSE
RetrocopyGIVDESQQAYQEAFEISKKQMQSTNPIRLGLALNFSS<FYFEILNSPEKACSLAKTAFDEAIAELDTLSE
ParentalESYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN
ESYKDSTLIMQLLRDNLTLWTSDTQG.EAEAGEGG.N
RetrocopyESYKDSTLIMQLLRDNLTLWTSDTQGEEAEAGEGGGN

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .16 RPM 193 .12 RPM
SRP051959_heart 0 .65 RPM 83 .65 RPM
SRP051959_kidney 0 .18 RPM 95 .67 RPM
SRP051959_liver 0 .06 RPM 35 .35 RPM
SRP051959_lung 0 .23 RPM 127 .44 RPM
SRP051959_lymph_node 0 .11 RPM 172 .46 RPM
SRP051959_skeletal_muscle 0 .00 RPM 32 .15 RPM
SRP051959_spleen 0 .15 RPM 136 .22 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1769 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1769 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1769 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 36 parental genes, and 137 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086942 retrocopies
Ailuropoda melanoleuca ENSAMEG000000003281 retrocopy
Bos taurus ENSBTAG000000002364 retrocopies
Canis familiaris ENSCAFG000000005806 retrocopies
Choloepus hoffmanni ENSCHOG000000027989 retrocopies
Callithrix jacchus ENSCJAG000000063942 retrocopies
Callithrix jacchus ENSCJAG00000015844 5 retrocopies
Callithrix jacchus ENSCJAG000000176642 retrocopies
Cavia porcellus ENSCPOG000000202855 retrocopies
Dasypus novemcinctus ENSDNOG0000000167210 retrocopies
Equus caballus ENSECAG000000218823 retrocopies
Ficedula albicollis ENSFALG000000058601 retrocopy
Felis catus ENSFCAG000000320174 retrocopies
Homo sapiens ENSG000001649241 retrocopy
Gallus gallus ENSGALG000000107251 retrocopy
Gorilla gorilla ENSGGOG000000221339 retrocopies
Loxodonta africana ENSLAFG000000049442 retrocopies
Myotis lucifugus ENSMLUG000000173233 retrocopies
Macaca mulatta ENSMMUG000000064897 retrocopies
Monodelphis domestica ENSMODG000000061588 retrocopies
Mustela putorius furoENSMPUG000000151584 retrocopies
Mus musculus ENSMUSG000000222853 retrocopies
Nomascus leucogenys ENSNLEG000000032207 retrocopies
Oryctolagus cuniculus ENSOCUG000000007342 retrocopies
Ochotona princeps ENSOPRG000000002763 retrocopies
Procavia capensis ENSPCAG000000107441 retrocopy
Pongo abelii ENSPPYG000000187917 retrocopies
Pelodiscus sinensis ENSPSIG000000037031 retrocopy
Pteropus vampyrus ENSPVAG000000166411 retrocopy
Sarcophilus harrisii ENSSHAG000000126712 retrocopies
Sus scrofa ENSSSCG000000060622 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000238643 retrocopies
Taeniopygia guttata ENSTGUG000000120781 retrocopy
Tarsius syrichta ENSTSYG0000000615010 retrocopies
Tursiops truncatus ENSTTRG000000159064 retrocopies
Vicugna pacos ENSVPAG000000058651 retrocopy



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