RetrogeneDB ID:

retro_cjac_685

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:10:48483577..48484471(+)
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:ENSCJAG00000004644
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_685
ATGGACCCCTGCAAAGTGAACGAGCTTCACGCCTTTGTGAAGATGTGTAAGTAGGATCCAAGCATTCTGCACACTGAGGA
AATGTGCTTCCTGAGGGAGTGGGTGGAGAGTATGGGGGCTAAAATACTACCTGCTACTCAGAAAGCTAAATCAGAAGAAA
ATGGCAAGGAAGAAAAACCTGATAGTAAGAAGGTGGAGGAAGACTTAAAGGCAGATGAACCATCAAGTGAGGAAAGTGAT
CTAGAAATTGATAATGAAGGTGTGATTGAATCAGACACCGATGCCCCTCGAGAAATGGGAGATGAAAATGCAGAGATAAG
AGAGGAGATGATGGGACAGGCAAATGATGAGAAAGTGGCTGCTATTGAAGCCCTAAATGATGGTGAATTGTAGAAAGCCA
TTGACTTATTCACAGATGCCATCAGGTTGAATCCTCGCTTGGCCATTTTGTATGCCAAGAGGGCCAGTGTCTTCATCAAA
TTACGGAAGCCAAATGCTGCCATTCGAGACTGAGACAGAGCCATTGAAATAAATCCTGATTCAGCTCAGCCTTATAAGTG
GCAAGGGAAAGCACACAGACTTTTAGGCCACTGGGAGGAAGCAGCCCATGATCTTGCCCTTGCCTGTAAATTGGATTATG
ATGAAGATGTGAGTGCAATGCTGAAAGAAGTTCAACCTAGGGCACAGAAAATTGCAGAACATCAGAGAAAGTATGAGCAA
AAATGTGAAAAGCGAGAGATCAAAGAAAGAAAAGAAAGAGTTAAGAAGGCTTGAGAAGAGCATGAGCGAGCCCAGAGGGA
GGAAGAAGCCAGATGACAGTCAGGAGCTCAGTATGGCTCTTTTCCAGGTGGCTTTTCTAGGGGAATGCCTGGAATGGCCA
GAATGCCTGGACTC

ORF - retro_cjac_685 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.67 %
Parental protein coverage: 81.3 %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDPRKVNELRAFVKMCKQDPSVLHTEEMRFLREWVESMGGKIPPATQKAKSEENTKEEKPDSKKVEEDLK
MDP.KVNEL.AFVKMCK.DPS.LHTEEM.FLREWVESMG.KI.PATQKAKSEEN.KEEKPDSKKVEEDLK
RetrocopyMDPCKVNELHAFVKMCK*DPSILHTEEMCFLREWVESMGAKILPATQKAKSEENGKEEKPDSKKVEEDLK
ParentalADEPSSEESDLEIDNEGVIEPDTDTPQEMGDENAEITEEMMDQANDKKVAAIEALNDGELQKAIDLFTDA
ADEPSSEESDLEIDNEGVIE.DTD.P.EMGDENAEI.EEMM.QAND.KVAAIEALNDGEL.KAIDLFTDA
RetrocopyADEPSSEESDLEIDNEGVIESDTDAPREMGDENAEIREEMMGQANDEKVAAIEALNDGEL*KAIDLFTDA
ParentalIKLNPRLAILYAKRASVFVKLQKPNAAIRDCDRAIEINPDSAQPYKWRGKAHRLLGHWEAAAHDLALACK
I.LNPRLAILYAKRASVF.KL.KPNAAIRD.DRAIEINPDSAQPYKW.GKAHRLLGHWE.AAHDLALACK
RetrocopyIRLNPRLAILYAKRASVFIKLRKPNAAIRD*DRAIEINPDSAQPYKWQGKAHRLLGHWEEAAHDLALACK
ParentalLDYDEDASAMLKEVQPRAQKIAEHRRKYERKREEREIKERIERVKKAREEHERAQREEEARRQSGAQYGS
LDYDED.SAMLKEVQPRAQKIAEH.RKYE.K.E.REIKER.ERVKKA.EEHERAQREEEAR.QSGAQYGS
RetrocopyLDYDEDVSAMLKEVQPRAQKIAEHQRKYEQKCEKREIKERKERVKKA*EEHERAQREEEAR*QSGAQYGS
ParentalFPGGFPGGMPGGFPGGMPGM
FPGGF..GMPG.....MPG.
RetrocopyFPGGFSRGMPG--MARMPGL

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 .73 RPM 51 .81 RPM
SRP051959_heart 0 .72 RPM 52 .32 RPM
SRP051959_kidney 0 .89 RPM 129 .52 RPM
SRP051959_liver 0 .45 RPM 118 .48 RPM
SRP051959_lung 0 .94 RPM 59 .25 RPM
SRP051959_lymph_node 1 .19 RPM 61 .85 RPM
SRP051959_skeletal_muscle 0 .48 RPM 80 .10 RPM
SRP051959_spleen 0 .67 RPM 61 .91 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_685 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_685 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_685 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 26 parental genes, and 148 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000052271 retrocopy
Ailuropoda melanoleuca ENSAMEG000000138801 retrocopy
Bos taurus ENSBTAG000000062024 retrocopies
Canis familiaris ENSCAFG0000000113914 retrocopies
Choloepus hoffmanni ENSCHOG000000126761 retrocopy
Callithrix jacchus ENSCJAG00000004644 11 retrocopies
Cavia porcellus ENSCPOG000000022904 retrocopies
Felis catus ENSFCAG000000118472 retrocopies
Homo sapiens ENSG0000010038016 retrocopies
Gorilla gorilla ENSGGOG0000002674716 retrocopies
Microcebus murinus ENSMICG000000088752 retrocopies
Myotis lucifugus ENSMLUG000000077642 retrocopies
Macaca mulatta ENSMMUG000000191183 retrocopies
Monodelphis domestica ENSMODG000000130422 retrocopies
Mustela putorius furoENSMPUG0000001643215 retrocopies
Mus musculus ENSMUSG000000224032 retrocopies
Nomascus leucogenys ENSNLEG0000001537817 retrocopies
Otolemur garnettii ENSOGAG000000169321 retrocopy
Pongo abelii ENSPPYG0000001185814 retrocopies
Pelodiscus sinensis ENSPSIG000000045531 retrocopy
Pteropus vampyrus ENSPVAG000000119082 retrocopies
Rattus norvegicus ENSRNOG000000190708 retrocopies
Sarcophilus harrisii ENSSHAG000000003192 retrocopies
Sus scrofa ENSSSCG000000000711 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000031651 retrocopy
Tursiops truncatus ENSTTRG000000115105 retrocopies



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