RetrogeneDB ID:

retro_cjac_968

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:12:32774235..32775408(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF2A
Ensembl ID:ENSCJAG00000001199
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_968
TATGTTCCAGGGAGTAGGGATGCAACTTCATTTGTTGCATTATATTTGTACCCCGACTTTGTTAGACCTCATGCAGCTTT
AGCCAACAGCAATTTCTCTAAGCCAATGACATTACAATGCTGTGGAATGAAAAAGCCACTGCTGGCTTGTAATAGTAAGA
ACAGATGTTGACAAGAGAACTTCCTGCTATGGGGAACAAAGGCTGAATTACACTGCAACAAATGGAGAAAGTTCTGTCAT
TTGTTCAATTACCAAAACGTAGCCCCATTTATGATATAATTTGGAAATCTGGTTCTACTGAGTTTTATGCTATTTATAGT
TTTATGCTTGCCAAAGCTATGATTTTCAACTTGAAATGTGATCTTGTGTTTGACCTTGGAACTGGTGCTCTAAGGCAGCC
TATTTGGCCTTTGTGGCCAGGTATTAATACTAACTGGATTTGGAAATCTGAGGGACAGACACGAGTGTGGGATATTAAAA
GCTACAAACTTATTTCCAAACAAGTAGCCTCTGATCCTGCATATTTTGCTAGGTACCTATAAGGGAGCACATTTTACTAC
CACACATGCTCCCAGGTTGTGTGTTAATAATGGACACAAGCTTTGGCATTATATCAGCCCTATCCTGAATGAGTAAGATA
TGTCATCAAATGCAGAAATAAGGCAGGTTTCTTGGCAGCCATTTCTGGATGGACTATTTCCAGCAAAAGCGGTAACTTTT
CAAGCAGTTCCAAGTCAAGTACCCAACTAGGAACCTAAATTTGCAGTTACTGATAGACTCCCAGCTTTAAGAAATAAACC
AATCAACAATTCCAAGCTGCATCAAGAGAAATCACCCCAGAATAAGAAATCACAACCAGGAAATGATAAACCATTATCAA
AAGCAGCCCTTAACAAATCAAAGGAAATATGAAGCTGAGAAAGCTACAAAGCAGGAAGTAAGAAGTGACGAGTCCAGATT
TGACACCTACCCTGTCCCACAGAGCACACCCTGAAATACAGGGTCTCGGTTAATGTCTGGAAACCCTGAGATAGACGAAA
AATTCAAGAACTGAAAAAGACAAAAGCAACTGAACCTTGAAAGAACACAGCAACTGAAACGCAGCCAGAAAAACAATGAG
TTAGAAAAATAAAAGATATTTCTCTTCTCCAAGAGCTGGAAGATTTGAAAATG

ORF - retro_cjac_968 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.25 %
Parental protein coverage: 66.39 %
Number of stop codons detected: 6
Number of frameshifts detected 10


Retrocopy - Parental Gene Alignment:

ParentalYVPGSKGAPSFVRLYQYPNFAGPHAALANKSFFK-ADKVTMLWNKKATAVL-VIASTEVDKTGASYYGEQ
YVPGS..A.SFV.LY.YP.F..PHAALAN..F.K.A...TMLWN.KATA.L.VI..T.VDK...S.YGEQ
RetrocopyYVPGSRDATSFVALYLYPDFVRPHAALANSNFSK<ANDITMLWNEKATAGL<VIVRTDVDKR-TSCYGEQ
ParentalTLHYIATNGESAVV-QLPKNGP-IYDVVWNSSSTEFCAVYGFMPAKATIFNLKCDPVFDFGTGP-RNAAY
.L.Y.ATNGES.V.....K..P.IYD..W.S.STEF.A.Y.FM.AKA.IFNLKCD.VFD.GTG....AAY
RetrocopyRLNYTATNGESSVICSITKT*P>IYDIIWKSGSTEFYAIYSFMLAKAMIFNLKCDLVFDLGTGA<SKAAY
Parental-YSPHGHILVLAGFGNLR-GQMEVWDVKNYKLISKPVASDSTYFAW-CPDGEHIL-TATCAPRLRVNNGY
.....G..L.L.GFGNLR.GQ..VWD.K.YKLISK.VASD..YFA...P..EHIL.T.T.APRL.VNNG.
Retrocopy<FGLCGQVLILTGFGNLR<GQTRVWDIKSYKLISKQVASDPAYFAR<VPIREHIL<TTTHAPRLCVNNGH
ParentalKIWHYTGSILHKYDVPSNAELWQVSWQPFLDGIFPAKTITYQAVPSEVPNEEPKVATAYRPPALRNKPIT
K.WHY...IL...D..SNAE..QVSWQPFLDG.FPAK..T.QAVPS.VPN.EPK.A...R.PALRNKPI.
RetrocopyKLWHYISPILNE*DMSSNAEIRQVSWQPFLDGLFPAKAVTFQAVPSQVPN*EPKFAVTDRLPALRNKPIN
ParentalNSKLHEEEPPQNMKPQSGNDKPLSKTALK-NQRKHEAKKAAKQEARSDKSPDLTPTPAPQSTPRSTISQS
NSKLH.E..PQN.K.Q.GNDKPLSK.AL..NQRK.EA.KA.KQE.RSD.S......P.PQSTP..T.S..
RetrocopyNSKLHQEKSPQNKKSQPGNDKPLSKAALN>NQRKYEAEKATKQEVRSDES-RFDTYPVPQSTP*NTGSRL
ParentalISGDPEIDKKIKN-LKKKLKAIEQLKEQAATGKQLEKNQLEKIQKETALLQELEDLEL
.SG.PEID.K.KN.LK.K.KA.E..K...AT..Q.EK....KI.K...LLQELEDL..
RetrocopyMSGNPEIDEKFKN<LK-KTKATEP*K-NTATETQPEKQ*VRKI-KDISLLQELEDLKM

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 28 .80 RPM
SRP051959_heart 0 .00 RPM 35 .68 RPM
SRP051959_kidney 0 .00 RPM 34 .61 RPM
SRP051959_liver 0 .00 RPM 66 .43 RPM
SRP051959_lung 0 .00 RPM 28 .87 RPM
SRP051959_lymph_node 0 .00 RPM 33 .06 RPM
SRP051959_skeletal_muscle 0 .00 RPM 59 .62 RPM
SRP051959_spleen 0 .00 RPM 34 .10 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_968 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_968 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_968 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000001199 1 retrocopy
retro_cjac_968 ,
Dasypus novemcinctus ENSDNOG000000140021 retrocopy
retro_dnov_1148,
Homo sapiens ENSG000001448951 retrocopy
retro_hsap_565,
Gorilla gorilla ENSGGOG000000153911 retrocopy
retro_ggor_509,
Loxodonta africana ENSLAFG000000037671 retrocopy
retro_lafr_502,
Macaca mulatta ENSMMUG000000176961 retrocopy
retro_mmul_2395,
Nomascus leucogenys ENSNLEG000000032191 retrocopy
retro_nleu_2213,
Oryctolagus cuniculus ENSOCUG000000160953 retrocopies
retro_ocun_1771, retro_ocun_1825, retro_ocun_1861,
Pongo abelii ENSPPYG000000296362 retrocopies
retro_pabe_517, retro_pabe_652,
Pan troglodytes ENSPTRG000000155281 retrocopy
retro_ptro_423,
Ictidomys tridecemlineatus ENSSTOG000000033741 retrocopy
retro_itri_1706,


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