RetrogeneDB ID:

retro_pabe_33

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:57618949..57619726(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000020403
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SPIN1
Ensembl ID:ENSPPYG00000019355
Aliases:SPIN1, SPIN, Spindlin-1
Description:Spindlin-1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R997]


Retrocopy-Parental alignment summary:






>retro_pabe_33
ATGAAGACCCCGTTTGGAAAGGCAGCTGCAGGGCAGCGGTCCAGGACAGGCGCTGGCCACGGCAGTGTGTCTGTTACCAT
GATAAAGAGGAAGGCTGCACACAAGAAGCATAGGAGCCGACCCACCTCCCAGCCTCGGAGGAACATCGTGGGCTGCAGAA
TTCAGCACGGATGGAAAGATGGAGATGAACCTCTAACACAGTGGAAAGGAACCGTTCTGGATCAGGTACCTGTAAATCCC
TCTCTGTATCTTATCAAATATGATGGATTTGACTGTGTTTATGGATTGGAACTTCACAGAGATGAAAGAGTGTCATCACT
TGAAGTCCTTCCTAATAGAGTTGCATCATCTAGAATCAGTGATACACACTTGGCAGAAATAATGGTTGGCAAAGCAGTGG
AACATATTTTTGAGACAGAGGAAGGTTCCAAAAATGAATGGAGGGGGATGGTCTTAGCTCAGGCACCTGTCATGAACACA
TGGTTTTACATTACCTATGAGAAAGATCCTGTATTATATATGTACCAGCTCTTAGATGATTATAAAGATGGTGACCTCCG
CATCCTTCAAGATTCCAATGATTCTCCTCTGGCAGAGAGGGAGCCAGGAGAAGTCATAGACAGCCTGGTAGGCAAACAGG
TGGAATACGCCAAAGACGATGGCTCCAAGAGAACTGGCATGGTCATTCATCAGGTAGAAGCAAAACCCTCTGTGTACTTC
ATCAAATTTGATGATGATTTCCATATCTATGTCTACGATTTGGTAAAAACATCTTAG

ORF - retro_pabe_33 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.48 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKTPFGKTPGQRSRADAGHAGVSANMMKKRTSHKKHRSSVGPSKPVSQPRRNIVGCRIQHGWKEGNGPVT
MKTPF....G..........G.............K.......S.P.SQPRRNIVGCRIQHGWK.G..P.T
RetrocopyMKTPF----GKAAAGQRSRTGAGHGSVSVTMIKRKAAHKKHRSRPTSQPRRNIVGCRIQHGWKDGDEPLT
ParentalQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHM
QWKGTVLDQVPVNPSLYLIKYDGFDCVYGLEL..DERVS.LEVLP.RVA.SRISD.HLA..M.GKAVEH.
RetrocopyQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELHRDERVSSLEVLPNRVASSRISDTHLAEIMVGKAVEHI
ParentalFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVV
FETE.GSK.EWRGMVLA.APVMNTWFYITYEKDPVLYMYQLLDDYK.GDLRI..DSNDSP.AEREPGEV.
RetrocopyFETEEGSKNEWRGMVLAQAPVMNTWFYITYEKDPVLYMYQLLDDYKDGDLRILQDSNDSPLAEREPGEVI
ParentalDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS
DSLVGKQVEYAK.DGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS
RetrocopyDSLVGKQVEYAKDDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

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
SRP007412_brain_prefrontal_cortex 3 .15 RPM 129 .88 RPM
SRP007412_cerebellum 4 .86 RPM 82 .20 RPM
SRP007412_heart 0 .60 RPM 23 .36 RPM
SRP007412_kidney 0 .99 RPM 58 .50 RPM
SRP007412_liver 0 .89 RPM 19 .59 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_33 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_33 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_33 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000033014 retrocopies
retro_amel_1831, retro_amel_1879, retro_amel_38, retro_amel_41,
Bos taurus ENSBTAG000000030444 retrocopies
retro_btau_1678, retro_btau_1841, retro_btau_187, retro_btau_553,
Canis familiaris ENSCAFG000000022083 retrocopies
retro_cfam_153, retro_cfam_2095, retro_cfam_59,
Choloepus hoffmanni ENSCHOG000000069832 retrocopies
retro_chof_1343, retro_chof_1852,
Callithrix jacchus ENSCJAG000000174521 retrocopy
retro_cjac_227,
Cavia porcellus ENSCPOG000000007431 retrocopy
retro_cpor_123,
Echinops telfairi ENSETEG000000137191 retrocopy
retro_etel_28,
Felis catus ENSFCAG000000071972 retrocopies
retro_fcat_32, retro_fcat_70,
Homo sapiens ENSG000001067231 retrocopy
retro_hsap_64,
Loxodonta africana ENSLAFG000000274972 retrocopies
retro_lafr_18, retro_lafr_58,
Microcebus murinus ENSMICG000000145101 retrocopy
retro_mmur_8,
Myotis lucifugus ENSMLUG000000085162 retrocopies
retro_mluc_132, retro_mluc_1626,
Mustela putorius furoENSMPUG000000085851 retrocopy
retro_mputfur_139,
Mus musculus ENSMUSG000000213953 retrocopies
retro_mmus_112, retro_mmus_16, retro_mmus_3351,
Oryctolagus cuniculus ENSOCUG000000118801 retrocopy
retro_ocun_63,
Otolemur garnettii ENSOGAG000000021662 retrocopies
retro_ogar_2327, retro_ogar_9,
Procavia capensis ENSPCAG000000158001 retrocopy
retro_pcap_14,
Pongo abelii ENSPPYG00000019355 1 retrocopy
retro_pabe_33 ,
Pan troglodytes ENSPTRG000000210882 retrocopies
retro_ptro_116, retro_ptro_95,
Pteropus vampyrus ENSPVAG000000133913 retrocopies
retro_pvam_2, retro_pvam_22, retro_pvam_858,
Rattus norvegicus ENSRNOG000000111194 retrocopies
retro_rnor_1483, retro_rnor_1531, retro_rnor_281, retro_rnor_2818,
Ictidomys tridecemlineatus ENSSTOG000000291071 retrocopy
retro_itri_136,
Tursiops truncatus ENSTTRG000000056026 retrocopies
retro_ttru_1061, retro_ttru_13, retro_ttru_1452, retro_ttru_1506, retro_ttru_1669, retro_ttru_1698,


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