RetrogeneDB ID:

retro_ptro_1150

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:16:69098156..69099555(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NONO
Ensembl ID:ENSPTRG00000022010
Aliases:None
Description:non-POU domain containing, octamer-binding [Source:HGNC Symbol;Acc:7871]


Retrocopy-Parental alignment summary:






>retro_ptro_1150
ATGCAGAGTAATAAAACTTTTAACTTGGAGAAGCAAAACCATACTCCAAGAAAGCATCATCAACATCATCACCAGCAGCA
ACAGCTGCAGCCGCCACCACCGCCAATACCTGCAAATGGGCAACAGGCCAGCAGCCAAAATGAAGGCTTGACTATTTGAC
CTGAAGAATTTTAGAAAACCAGGAGAGAAGACCTTGACCCAACGAAGCCGTCTTTTTGTGGGAAATCTTCCTCCCGACAT
CACTGAGGAAGAAATGAGGAAACTATTTGAGAAATATGGAAAGGCAGGCGAAGTCTTCATTCATAAGGATTAAGGATTTG
GCTTTATCCGCTTGGAAACACGAACCCTAGCGGAGATTGCGAAAGTGGAGCTGGACGGTATGCCACTCTGTGGAAAGCAG
CTGCGTGTGCGCTTTTCCTGCCATAGTGCATCCCTTACAGTTCGAAACCTTCCTCAGTATGTGTCCAACGAAGTGCTGGA
AGAAGCCTTTTCTGTGTTTGGCCAGGTAGAGAGGGCTGTAGTCATTGTGGATGATCGAGGAAGGCCCTCAGGAAAAGGCA
TTGTTGAGTTCTCAGGGAAGCCAGCTGCTGGGAAAGCTCTGGACAGACGCAGTGAAGGCTCCTTCCTGCTAACCACATTT
CCTCGTCCTGTGACTATGGAGCCCATGGACCAGTTAGATGATGAAGGGGGACTTCCAGAGAAGCTGGTTATAAAAAACCA
GCAATTTCACAAGGAACGAGAGCAACCACCCAGATTTGCACAGCCTGGCTCCTTTGAGTGTGAATATGCCATGCGCTGGA
AGGCACTCATTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACCGCAACATCAAGGAGGCTCGTGAGAAGCCAGAGATG
GAGATGGAGGCTGCACGCCATAAGCACCAGGTCATGGTAATGAGACAGAATTTGATGAGGCGCCAAGAAGAACTTCGGAG
GATGGAAGAGCTGCACAACCAAGAGGTGCAAAAACGAAAGCAACTGGAGCTCAGGCAGGAGGAAGAGCGCAGGCGCCGTG
AAGAAGAGATGCGGCGGCAGCAAGAAGAAATGATGCAGCCACAGCAGGAAGGATTCAAGGGAACCTTCCCTGATGTGAGA
GAGCAGGAGATTTGGATGGGTCAGATGGCTATGGGAGGTGCTATGGGCATAAACAGCAGAGGTGCTTTGACCCCTGCTCC
TGTGCCAGCTGGTACCCCAGCTCCTCCAGGACCTGCCACTATGATGCCGGATGGAACTTTGGGATTGACCCCACCAACAA
CTGAACGCTTTGGTCAGGCTGCTACAATGGAAGGAATTGGGGCAATTGGTGAAACTCCTCCTGCATTCAACCATGCAGCT
CCTGGAGCTGAATTTGCTCCAAACAAACGTCGCCGATAC

ORF - retro_ptro_1150 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.83 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMQSNKTFNLEKQNHTPRKHHQHHHQQQHHQQQQQQPPPPPIPANGQQASSQNEGLTI-DLKNFRKPGEKT
MQSNKTFNLEKQNHTPRKHHQHHHQQQ....Q.Q.P.PPPIPANGQQASSQNEGLTI.DLKNFRKPGEKT
RetrocopyMQSNKTFNLEKQNHTPRKHHQHHHQQQ----QLQPP-PPPIPANGQQASSQNEGLTI>DLKNFRKPGEKT
ParentalFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL
.TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD.GFGFIRLETRTLAEIAKVELD.MPL.GKQL
RetrocopyLTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD*GFGFIRLETRTLAEIAKVELDGMPLCGKQL
ParentalRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCS
RVRF.CHSASLTVRNLPQYVSNE.LEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAA.KALDR.S
RetrocopyRVRFSCHSASLTVRNLPQYVSNEVLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAAGKALDRRS
ParentalEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEK
EGSFLLTTFPRPVT.EPMDQLDDE.GLPEKLVIKNQQFHKEREQPPRFAQPGSFE.EYAMRWKALIEMEK
RetrocopyEGSFLLTTFPRPVTMEPMDQLDDEGGLPEKLVIKNQQFHKEREQPPRFAQPGSFECEYAMRWKALIEMEK
ParentalQQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERR
QQQDQVDRNIKEAREK.EMEMEAARH.HQVM.MRQ.LMRRQEELRRMEELHNQEVQKRKQLELRQEEERR
RetrocopyQQQDQVDRNIKEAREKPEMEMEAARHKHQVMVMRQNLMRRQEELRRMEELHNQEVQKRKQLELRQEEERR
ParentalRREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPGPATM
RR..................FKGTFPD.REQEI.MGQMAMGGAMGIN.RGA..PAPVPAGTPAPPGPATM
RetrocopyRRXXXXXXXXXXXXXXXXXXFKGTFPDVREQEIWMGQMAMGGAMGINSRGALTPAPVPAGTPAPPGPATM
ParentalMPDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
MPDGTLGLTPPTTERFGQAATMEGIGAIG.TPPAFN.AAPGAEFAPNKRRRY
RetrocopyMPDGTLGLTPPTTERFGQAATMEGIGAIGETPPAFNHAAPGAEFAPNKRRRY

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 0 .18 RPM 66 .28 RPM
SRP007412_cerebellum 0 .22 RPM 178 .45 RPM
SRP007412_heart 0 .06 RPM 57 .74 RPM
SRP007412_kidney 0 .18 RPM 133 .11 RPM
SRP007412_liver 0 .20 RPM 114 .96 RPM
SRP007412_testis 0 .21 RPM 44 .37 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_1150 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1150 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1150 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1699
Gorilla gorilla retro_ggor_1273
Pongo abelii retro_pabe_1398
Parental genes homology:
Parental genes homology involve 21 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160572 retrocopies
retro_amel_1438, retro_amel_795,
Bos taurus ENSBTAG000000121522 retrocopies
retro_btau_1027, retro_btau_313,
Canis familiaris ENSCAFG000000170711 retrocopy
retro_cfam_98,
Callithrix jacchus ENSCJAG000000367441 retrocopy
retro_cjac_3990,
Equus caballus ENSECAG000000085022 retrocopies
retro_ecab_357, retro_ecab_427,
Felis catus ENSFCAG000000148072 retrocopies
retro_fcat_1219, retro_fcat_147,
Homo sapiens ENSG000001471401 retrocopy
retro_hsap_1699,
Gorilla gorilla ENSGGOG000000061941 retrocopy
retro_ggor_1273,
Microcebus murinus ENSMICG000000002321 retrocopy
retro_mmur_569,
Myotis lucifugus ENSMLUG000000024891 retrocopy
retro_mluc_622,
Mustela putorius furoENSMPUG000000049371 retrocopy
retro_mputfur_937,
Mus musculus ENSMUSG000000313112 retrocopies
retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys ENSNLEG000000012781 retrocopy
retro_nleu_1344,
Oryctolagus cuniculus ENSOCUG000000218482 retrocopies
retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii ENSOGAG000000048343 retrocopies
retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii ENSPPYG000000204511 retrocopy
retro_pabe_1398,
Pan troglodytes ENSPTRG00000022010 1 retrocopy
retro_ptro_1150 ,
Pteropus vampyrus ENSPVAG000000165031 retrocopy
retro_pvam_444,
Rattus norvegicus ENSRNOG000000036892 retrocopies
retro_rnor_1178, retro_rnor_1503,
Sorex araneus ENSSARG000000079592 retrocopies
retro_sara_661, retro_sara_663,
Drosophila melanogaster FBgn00042271 retrocopy
retro_dmel_11,


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