RetrogeneDB ID:

retro_hsap_1699

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:69790440..69791840(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000260290
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NONO
Ensembl ID:ENSG00000147140
Aliases:NONO, NMT55, NRB54, P54, P54NRB
Description:non-POU domain containing, octamer-binding [Source:HGNC Symbol;Acc:7871]


Retrocopy-Parental alignment summary:






>retro_hsap_1699
ATGCAGAGTAATAAAACTTTTAACTTGGAGAAGCAAAACCATACTCCAAGAAAGCATCATCAACATCACCACCAGCAGCA
ACAGCTGCAGCCGCCACCACCGCCAATACCTGCAAATGGGCAACAGGCCAGCAGCCAAAATGAAGGCTTTGACTATTTGG
CCTGAAGAATTTTAGAAAACCAGGAGAGAAGACCTTCACCCAACGAAGCCGTCTTTTTGTGGGAAATCTTCCTCCCGACA
TCACTGAGGAAGAAATGAGGAAACTATTTGAGAAATATGGAAAGGCAGGCGAAGTCTTCATTCATAAGGATTAAGGATTT
GGCTTTATCCGCTTGGAAACACGAACCCTAGCGGAGATTGCGAAAGTGGAGCTGGACAATATGCCACTCTGTGGAAAGCA
GCTGCGTGTGCGCTTTTCCTGCCATAGTGCATCCCTTACAGTTCGAAACCTTCCTCAGTATGTGTCCAACGAAGTGCTGG
AAGAAGCCTTTTCTGTGTTTGGCCAGGTAGAGAGGGCTGTAGTCATTGTGGATGATCGAGGAAGGCCCTCAGGAAAAGGC
ATTGTTGAGTTCTCAGGGAAGCCAGCTGCTGGGAAAGCTCTGGACAGACGCAGTGAAGGCTCCTTCCTGCTAACCACATT
TCCTCGTCCTGTGACTATGGAGCCCATGGACCAGTTAGATGATGAAGGGGGACTTCCAGAGAAGCTGGTTATAAAAAACC
AGCAATTTCACAAGGAACGAGAGCAACCACCCAGATTTGCACAGCCTGGCTCCTTTGAGTATGAATATGCCATGCGCTGG
AAGGCACTCATTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACCGCAACATCAAAGAGGCTCGTGAGAAGCCAGAGAT
GGAGATGGAGGCTGCACGCCATAAGCACCAGGTCATGCTAATGAGACAGAATTTGATGAGGCGCCAAGAAGAACTTCGGA
GGATGGAAGAGCTGCACAACCAAGAGGTGCAAAAACGAAAGCAACTGGAGCTCAGGCAGGAGGAAGAGCGCAGGCGCCCT
GAAGAAGAGATGCGGCGGCAGCAAGAAGAAATGATGCAGCCACAGCAGGAAGGATTCAAGGGAACCTTCCCTGATGTGAG
AGAGCAGGAGATTTGGATGGGTCAGATGGCTATGGGAGGTGCTATGGGCATAAACAGCAGAGGTGCCTTGACCCCTGCTC
CTGTGCCAGCTGGTACCCCAGCTCCTCCAGGACCTGCCACTATGATGCCGGATGGAACTTTGGGATTGACCCCACCAACA
ACTGAACGCTTTGGTCAGGCTGCTACAATGGAAGGAATTGGGGCAATTGGTGAAACTCCTCCTGCATTCAACCATGCAGC
TCCTGGAGCTGAATTTGCTCCAAACAAACGTCGCCGATAC

ORF - retro_hsap_1699 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.06 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMQSNKTFNLEKQNHTPRKHHQHHHQQQHHQQQQQQPPPPPIPANGQQASSQNEG-LTI-DLKNFRKPGEK
MQSNKTFNLEKQNHTPRKHHQHHHQQQ....Q.Q.P.PPPIPANGQQASSQNEG.LTI..LKNFRKPGEK
RetrocopyMQSNKTFNLEKQNHTPRKHHQHHHQQQ----QLQPP-PPPIPANGQQASSQNEG>LTI>GLKNFRKPGEK
ParentalTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQ
TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD.GFGFIRLETRTLAEIAKVELDNMPL.GKQ
RetrocopyTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD*GFGFIRLETRTLAEIAKVELDNMPLCGKQ
ParentalLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRC
LRVRF.CHSASLTVRNLPQYVSNE.LEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAA.KALDR.
RetrocopyLRVRFSCHSASLTVRNLPQYVSNEVLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAAGKALDRR
ParentalSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEME
SEGSFLLTTFPRPVT.EPMDQLDDE.GLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEME
RetrocopySEGSFLLTTFPRPVTMEPMDQLDDEGGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEME
ParentalKQQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEER
KQQQDQVDRNIKEAREK.EMEMEAARH.HQVMLMRQ.LMRRQEELRRMEELHNQEVQKRKQLELRQEEER
RetrocopyKQQQDQVDRNIKEAREKPEMEMEAARHKHQVMLMRQNLMRRQEELRRMEELHNQEVQKRKQLELRQEEER
ParentalRRREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPGPAT
RR...................FKGTFPD.REQEI.MGQMAMGGAMGIN.RGA..PAPVPAGTPAPPGPAT
RetrocopyRRPXXXXXXXXXXXXXXXXXXFKGTFPDVREQEIWMGQMAMGGAMGINSRGALTPAPVPAGTPAPPGPAT
ParentalMMPDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
MMPDGTLGLTPPTTERFGQAATMEGIGAIG.TPPAFN.AAPGAEFAPNKRRRY
RetrocopyMMPDGTLGLTPPTTERFGQAATMEGIGAIGETPPAFNHAAPGAEFAPNKRRRY

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
bodymap2_adipose 0 .16 RPM 219 .73 RPM
bodymap2_adrenal 0 .06 RPM 212 .51 RPM
bodymap2_brain 0 .07 RPM 80 .73 RPM
bodymap2_breast 0 .06 RPM 175 .66 RPM
bodymap2_colon 0 .02 RPM 176 .52 RPM
bodymap2_heart 0 .00 RPM 70 .17 RPM
bodymap2_kidney 0 .08 RPM 155 .74 RPM
bodymap2_liver 0 .06 RPM 96 .87 RPM
bodymap2_lung 0 .11 RPM 137 .20 RPM
bodymap2_lymph_node 0 .02 RPM 211 .65 RPM
bodymap2_ovary 0 .15 RPM 373 .01 RPM
bodymap2_prostate 0 .12 RPM 228 .49 RPM
bodymap2_skeletal_muscle 0 .11 RPM 86 .59 RPM
bodymap2_testis 0 .08 RPM 197 .66 RPM
bodymap2_thyroid 0 .06 RPM 208 .71 RPM
bodymap2_white_blood_cells 0 .37 RPM 271 .48 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1699 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1699 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_534851016 libraries721 libraries91 libraries1 library0 libraries
TSS #2 TSS_53486187 libraries150 libraries1139 libraries320 libraries33 libraries
TSS #3 TSS_53487997 libraries779 libraries51 libraries0 libraries2 libraries

The graphical summary, for retro_hsap_1699 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_1699 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1699 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1150
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 ENSG00000147140 1 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 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,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.63 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .17 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .49 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .25 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .63 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .35 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .16 RPM
FIN_HG00277 0 .41 RPM
FIN_HG00315 0 .19 RPM
FIN_HG00321 0 .21 RPM
FIN_HG00328 0 .54 RPM
FIN_HG00338 0 .28 RPM
FIN_HG00349 0 .26 RPM
FIN_HG00375 0 .29 RPM
FIN_HG00377 0 .25 RPM
FIN_HG00378 0 .34 RPM
GBR_HG00099 0 .35 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .22 RPM
GBR_HG00131 0 .17 RPM
GBR_HG00133 0 .31 RPM
GBR_HG00134 0 .20 RPM
GBR_HG00137 0 .16 RPM
GBR_HG00142 0 .22 RPM
GBR_HG00143 0 .26 RPM
TSI_NA20512 0 .23 RPM
TSI_NA20513 0 .29 RPM
TSI_NA20518 0 .44 RPM
TSI_NA20532 0 .17 RPM
TSI_NA20538 0 .46 RPM
TSI_NA20756 0 .58 RPM
TSI_NA20765 0 .29 RPM
TSI_NA20771 0 .23 RPM
TSI_NA20786 0 .31 RPM
TSI_NA20798 0 .25 RPM
YRI_NA18870 0 .58 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .21 RPM
YRI_NA19093 0 .10 RPM
YRI_NA19099 0 .48 RPM
YRI_NA19114 0 .26 RPM
YRI_NA19118 0 .19 RPM
YRI_NA19213 0 .45 RPM
YRI_NA19214 0 .17 RPM
YRI_NA19223 0 .32 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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