RetrogeneDB ID:

retro_pabe_1398

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:16:57229021..57230429(-)
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:ENSPPYG00000020451
Aliases:None
Description:non-POU domain-containing octamer-binding protein [Source:RefSeq peptide;Acc:NP_001124612]


Retrocopy-Parental alignment summary:






>retro_pabe_1398
ATGCACAGTAATAAAACTTTTAACTTGGAGAAGCAAAACCATACTCCAAGAAAGCATCATCAACGTCATCAACGTCACCA
CCAGCAGCAACACCAGCAGCCGCCACCACCGCCAATACCTGCAAATGGGCAACAGGTCAGCAGCCAAAATGAAGGCTTGG
CTATTTGACCTGAAGAATTTTAGAAAACCAGGAGAGAAGACCTTCACCCAATGAAGCCGTCTTTTTGTGGGAAATCTTCC
TCCCGACATCACTGAGGAAGAAATGAGGAAACTATTTAAGAAATATGGAAAGGCAGGCAAAGTCTTCATTCATAAGGATT
AAGGATTTGGCTTTATCCGCTTGGAAACACGAACCCTAGCGGAGATTGCGAAAGTGGAGCTGGACAATAAGCCACTCTGT
GGAAAGCAGCTGTGTGTGCACTTTTCCTGCCATAGTGCATCCCTTACAGTTCGAAACCTTCCTCAGTATGTGTCAAACGA
ACTGCTGGAAGAAGCCTTTTCTGTGTTTGGCCAGGTAGAGAGGGCTGTAGTCATTGTGGGTGATCGAGGAAGGCCCTCAG
GAAAAGGCATTGTTGAGTTCTCAGGGAAGCCAGCTGCTGGGAAAGCTCTGGACAGATGCAGTGAAGGCTCCTTCCTGCTA
ACCACATTTCTTTGTCCTGTGACTATGGAGCCCATGGACCAGTTAGATGATGAAGAGGGACTTCCAGAGAAGCTGGTTAT
AAAAAACCAGCGATTTCACAAGGAACGAGAGCAGCCACCCAGATTTGCACAACCTGGCTCCTTTGAGTATGAATATGCCA
TGCGCTGGAAGGCACTCACTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACCGCAACATCAAGGAGGCTCGTGAGAAG
CCGGAGATGGAGATGGAGGCTGCACGCCATAAGCACCAGGTCATGCTAATGAGACAGAATTTGACGAGGCGCCAAGAAGA
ACTTCGGAGGATGGAAGAGCTGCACAACCAAGAGGTGCAAAAACGAAAGCAACTGGAGCTCAGGCAGGAGGAAGGGCGCA
GGCGCCGTGAAGAAGAGATGCGGCGGCAGCAAGAAGAAACGATGCGGCGACAGCAGCAAGGATTCAAGCGAACCTTCCCT
GATGTGAGAGAGCAGGAGATTCGGATGGATCAGATGGCTATGGGAGGTGCTATGGGCATAAACAGCAGAGGTGCCTTGCC
CCCTGCTCCTGTGCCAGCTGGTACCCCGGCTCCTCCAGGACCTGCCACTATGATGCCGGATGGAACTTTGGGATTGACCC
CACAAACAACTGAACGCTTTGGTCAGGCTGCTACAATGGAAGGAATTGGGGCAATTTGTGGAACTCCGCCTGCATTCAAC
CATGCAGCTCCTGGAGCTGAATTTGCTCCAAACAAACGTCGCAGATAC

ORF - retro_pabe_1398 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.02 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMQSNKTFNLEKQNHTPRKHHQHHHQQQHHQQQQQQPPPPPIPANGQQASSQNEGLTI-DLKNFRKPGEKT
M.SNKTFNLEKQNHTPRK...........Q...QQPPPPPIPANGQQ.SSQNEGL.I.DLKNFRKPGEKT
RetrocopyMHSNKTFNLEKQNHTPRKXXXXXXXXHQQQ--HQQPPPPPIPANGQQVSSQNEGLAI>DLKNFRKPGEKT
ParentalFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL
FTQ.SRLFVGNLPPDITEEEMRKLF.KYGKAG.VFIHKD.GFGFIRLETRTLAEIAKVELDN.PL.GKQL
RetrocopyFTQ*SRLFVGNLPPDITEEEMRKLFKKYGKAGKVFIHKD*GFGFIRLETRTLAEIAKVELDNKPLCGKQL
ParentalRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCS
.V.F.CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIV.DRGRPSGKGIVEFSGKPAA.KALDRCS
RetrocopyCVHFSCHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVGDRGRPSGKGIVEFSGKPAAGKALDRCS
ParentalEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEK
EGSFLLTTF..PVT.EPMDQLDDEEGLPEKLVIKNQ.FHKEREQPPRFAQPGSFEYEYAMRWKAL.EMEK
RetrocopyEGSFLLTTFLCPVTMEPMDQLDDEEGLPEKLVIKNQRFHKEREQPPRFAQPGSFEYEYAMRWKALTEMEK
ParentalQQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERR
QQQDQVDRNIKEAREK.EMEMEAARH.HQVMLMRQ.L.RRQEELRRMEELHNQEVQKRKQLELRQEE.RR
RetrocopyQQQDQVDRNIKEAREKPEMEMEAARHKHQVMLMRQNLTRRQEELRRMEELHNQEVQKRKQLELRQEEGRR
ParentalRREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPASQGPATM
RR.................GFK.TFPD.REQEIRM.QMAMGGAMGIN.RGA.PPAPVPAGTPA..GPATM
RetrocopyRRXXXXXXXXXXXXXXXXQGFKRTFPDVREQEIRMDQMAMGGAMGINSRGALPPAPVPAGTPAPPGPATM
ParentalMPDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
MPDGTLGLTP.TTERFGQAATMEGIGAI.GTPPAFN.AAPGAEFAPNKRRRY
RetrocopyMPDGTLGLTPQTTERFGQAATMEGIGAICGTPPAFNHAAPGAEFAPNKRRRY

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 12 .83 RPM 65 .91 RPM
SRP007412_cerebellum 14 .59 RPM 64 .57 RPM
SRP007412_heart 5 .96 RPM 26 .76 RPM
SRP007412_kidney 15 .11 RPM 83 .33 RPM
SRP007412_liver 12 .55 RPM 54 .47 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_1398 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1398 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1398 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1699
Pan troglodytes retro_ptro_1150
Gorilla gorilla retro_ggor_1273
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 ENSPPYG00000020451 1 retrocopy
retro_pabe_1398 ,
Pan troglodytes ENSPTRG000000220101 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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