RetrogeneDB ID:

retro_cjac_4198

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:84812693..84813659(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000001728
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RNF2
Ensembl ID:ENSCJAG00000005442
Aliases:None
Description:ring finger protein 2 [Source:HGNC Symbol;Acc:10061]


Retrocopy-Parental alignment summary:






>retro_cjac_4198
AAAACATGGGAACTCAGTTTATATGAATTACAACGAACACCTCAGGAGGCAATAACAGATGCTTTAGAAATTGTGGTGTC
ACGTCGAAGTCTACACAGTGAATCTATGTGCCCAATTTGTTTGGATACGTTGAAGAATACTATGAATGACTACAAAGGAG
TGCATCGTTTTTGTGCAGACTGCATCATCACAGCCCTTAGAAGTGGCAACAAAGAATGTCCCACCTGTCGGAAAAAAACT
AGTTTCCAAAAAATCACTAAGGCCAGACCCGAACTTTGATACACTCATCAGCAAAATTTATCCACGTCATGATGAGTATG
AAGCTCATCAAGAGAGAGTATTAGCCAGTATCAACAAGCACGATAATCAGCAAGCACTCAGTCACAGCATTGGGGAAGGA
CTGATGATACAGGGCATGAATAGACTGCAGCGAGGCAAGAAACAACAGATTGAAAATGGCAGTGGAGCAGAAGATAATGG
TGACAGTTCACACTGTAGTAATGCCTCCACACACAGCAATCAGGAAGCAGGCCCTAGTAACAACGGACCAAAATATCTGA
TGATTCTGAGCTTGATATTGATCATAACAATGCAGCAGTGGCAATTGATCCAGTAATGGATGGTGCTGGTGAAACTGAAT
TAGTATTCAGGCCTCACCCTGCCCTTACGGACAAAGATGAGAGTATACAGACAAGGTACATAAAGACTTCAGATAACGCC
ACTGTTGATCACTTATCCAAGTATCTGACTGTGAGGTTAGCTTTAGAAGAACTTCAAAGCAAAGGTGAATCAAACCAGTT
GAACCTTGATACAGCCAGTGAGAAGCACTATACCATTTATATGGCAACAGCCAGTGACCAGTTCACTATATTAAATGGCT
CTTTTTCTTTTGAATTGGTGAGTGAGAAATACTGGAAAGTGAACAAACCTATGGAACTTTACCACGCACCTACAAAGGAG
CACAAA

ORF - retro_cjac_4198 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.42 %
Parental protein coverage: 95.83 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGN
KTWELSLYELQRTPQEAITD.LEIVVS.RSLHSE.MCPICLD.LKNTM......HRFCADCIITALRSGN
RetrocopyKTWELSLYELQRTPQEAITDALEIVVSRRSLHSESMCPICLDTLKNTMNDYKGVHRFCADCIITALRSGN
ParentalKECPTCRKK-LVSKRSLRPDPNFDALISKIYPSRDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAM
KECPTCRKK.LVSK.SLRPDPNFD.LISKIYP..DEYEAHQERVLA.INKH.NQQALSHSI.EGL.IQ.M
RetrocopyKECPTCRKK>LVSKKSLRPDPNFDTLISKIYPRHDEYEAHQERVLASINKHDNQQALSHSIGEGLMIQGM
ParentalNRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSN-KRTKTSDDSGLELDNNNAAVAIDPVMDG
NRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSN..RTK.SDDS.L..D.NNAAVAIDPVMDG
RetrocopyNRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSN<QRTKISDDSELDIDHNNAAVAIDPVMDG
ParentalASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYT
A.E.ELVFRPHP.L..KD.S.QTRYIKTS.NATVDHLSKYL.VRLALEEL.SKGESNQ.NLDTASEK.YT
RetrocopyAGETELVFRPHPALTDKDESIQTRYIKTSDNATVDHLSKYLTVRLALEELQSKGESNQLNLDTASEKHYT
ParentalIYIATASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK
IY.ATAS.QFT.LNGSFS.ELVSEKYWKVNKPMELY.APTKEHK
RetrocopyIYMATASDQFTILNGSFSFELVSEKYWKVNKPMELYHAPTKEHK

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 7 .06 RPM
SRP051959_heart 0 .00 RPM 15 .30 RPM
SRP051959_kidney 0 .02 RPM 14 .13 RPM
SRP051959_liver 0 .00 RPM 6 .87 RPM
SRP051959_lung 0 .00 RPM 13 .40 RPM
SRP051959_lymph_node 0 .00 RPM 13 .88 RPM
SRP051959_skeletal_muscle 0 .00 RPM 6 .11 RPM
SRP051959_spleen 0 .00 RPM 14 .18 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_4198 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_4198 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_4198 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000111993 retrocopies
retro_chof_1450, retro_chof_2217, retro_chof_2251,
Callithrix jacchus ENSCJAG00000005442 1 retrocopy
retro_cjac_4198 ,
Erinaceus europaeus ENSEEUG000000140911 retrocopy
retro_eeur_88,
Echinops telfairi ENSETEG000000158241 retrocopy
retro_etel_2081,
Felis catus ENSFCAG000000096091 retrocopy
retro_fcat_1725,
Homo sapiens ENSG000001214812 retrocopies
retro_hsap_4056, retro_hsap_4226,
Gorilla gorilla ENSGGOG000000144001 retrocopy
retro_ggor_2724,
Loxodonta africana ENSLAFG000000213571 retrocopy
retro_lafr_407,
Myotis lucifugus ENSMLUG000000011291 retrocopy
retro_mluc_2187,
Monodelphis domestica ENSMODG000000074221 retrocopy
retro_mdom_857,
Nomascus leucogenys ENSNLEG000000180292 retrocopies
retro_nleu_1042, retro_nleu_554,
Oryctolagus cuniculus ENSOCUG000000048921 retrocopy
retro_ocun_838,
Pongo abelii ENSPPYG000000004172 retrocopies
retro_pabe_3331, retro_pabe_3374,
Pan troglodytes ENSPTRG000000017752 retrocopies
retro_ptro_2749, retro_ptro_2871,
Ictidomys tridecemlineatus ENSSTOG000000066253 retrocopies
retro_itri_1646, retro_itri_1794, retro_itri_410,
Tupaia belangeri ENSTBEG000000163874 retrocopies
retro_tbel_1757, retro_tbel_3368, retro_tbel_3892, retro_tbel_4061,
Tarsius syrichta ENSTSYG000000061096 retrocopies
retro_tsyr_1344, retro_tsyr_1647, retro_tsyr_2063, retro_tsyr_2083, retro_tsyr_227, retro_tsyr_474,


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