RetrogeneDB ID:

retro_ptro_2348

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:45754876..45755535(+)
Located in intron of:ENSPTRG00000023379
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBM22
Ensembl ID:ENSPTRG00000017423
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2348
CAATCAGAATATTATGGAATCAATGATCCAGAAACAGATAAGCATCTAAAGTGGGCTTCAATCATGCCCCATCTGGACCC
ATCAGAGGACAAGGTTATCCTCCCCATATGTTGGTAGTCTGGATAATACCATTTCTGAGACAGATCTAAGACATCATCAC
TACCAGTTTGGAGAGATGCAGATTGATTACTGTTGTTCAGAGAGAGCAGTGTGCTTTCATCCAGGTTTCCACAGGGCAGG
CTGCAGAAGTGGCTGCTGAGAAGTCCTTTGATAAGTTGATTGTCAATGGCTGTAGACTCAACATAAAATGGGGAAGATCC
CAAGCATCCAGAGGAAAAGAAAAAGAGAAGAACAGATCACAGACTCTGGGATCCAGCTACAGCCTATTCCAGCACTGCCA
TGAGCTCTTCCTCCTCCTACAGCAGCAGCAGATGCATGTACCAACTACTTCAACCTGCCCCAACATGGTCCTCCAGCTGT
GGTGAACATTGCCCAGCCACCAGCCCCTAGTCTTCCACACCCCCAACCCCAGGATTTAGGCCACACATATTCACCTCAAT
GGGACCACCCTTTCCTTTCATGACAACTCCAGGATTAATCCACTATCTTTCTCATGACCTCAGAGGATGGGAGCTCATGC
CAGAAAACATAGGAAACCC

ORF - retro_ptro_2348 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.96 %
Parental protein coverage: 52.86 %
Number of stop codons detected: 1
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalKDRYYGINDPVADKLLKRASTMPRLDPPEDKTI-TTLYVGGLGDTITETDLRNHFYQFGEI-RTITVVQR
...YYGINDP..DK.LK.AS.MP.LD.P.........YVG.L..TI.ETDLR.H.YQFGE..R.ITVVQR
RetrocopyQSEYYGINDPETDKHLKWASIMPHLD-PSEDKV>SSPYVGSLDNTISETDLRHHHYQFGEM>RLITVVQR
ParentalQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGT-TDSGIKLEPVPGLPGAL
.QCAFIQ..T.QAAEVAAEKSF.KLIVNG.RLN.KWGRSQA.RGKEKEK....TDSGI.L.P.P.LP.AL
RetrocopyEQCAFIQVSTGQAAEVAAEKSFDKLIVNGCRLNIKWGRSQASRGKEKEKNRS<TDSGIQLQPIPALP*AL
ParentalPPPPAAEEEASANYFNLPPSGPPAVVNIALPPPPGI-APPPPPGFGPHMFHPMGPPPPFMRAPGPIHYPS
PPP.AA...A..NYFNLP..GPPAVVNIA.PP.P.....PP.PGF.PH.F..MGPP.PFM..PG.IHY.S
RetrocopyPPPTAA-ADACTNYFNLPQHGPPAVVNIAQPPAPSL<STPPTPGFRPHIFTSMGPPFPFMTTPGLIHYLS
ParentalQD-PQRMGAHAGKHSSP
.D.PQRMGAHA.KH..P
RetrocopyHD<PQRMGAHARKHRKP

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
SRP007412_brain_prefrontal_cortex 0 .04 RPM 24 .61 RPM
SRP007412_cerebellum 0 .00 RPM 42 .77 RPM
SRP007412_heart 0 .00 RPM 15 .16 RPM
SRP007412_kidney 0 .00 RPM 32 .25 RPM
SRP007412_liver 0 .00 RPM 19 .18 RPM
SRP007412_testis 0 .00 RPM 24 .55 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2348 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2348 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2348 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3465
Gorilla gorilla retro_ggor_2337
Pongo abelii retro_pabe_2861
Macaca mulatta retro_mmul_1762

Parental genes homology:
Parental genes homology involve 12 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000180821 retrocopy
Callithrix jacchus ENSCJAG000000209636 retrocopies
Cavia porcellus ENSCPOG000000019462 retrocopies
Dasypus novemcinctus ENSDNOG000000111661 retrocopy
Homo sapiens ENSG000000865892 retrocopies
Gorilla gorilla ENSGGOG000000129472 retrocopies
Myotis lucifugus ENSMLUG000000090402 retrocopies
Macaca mulatta ENSMMUG000000206834 retrocopies
Monodelphis domestica ENSMODG000000095741 retrocopy
Pongo abelii ENSPPYG000000159554 retrocopies
Pan troglodytes ENSPTRG00000017423 2 retrocopies
retro_ptro_2348 , retro_ptro_2898,
Tarsius syrichta ENSTSYG000000039393 retrocopies



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