RetrogeneDB ID:

retro_hsap_4

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:19049657..19050599(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000155876
Aliases:RRAGA, FIP-1, FIP1, RAGA
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RRAGB
Ensembl ID:ENSG00000083750
Aliases:RRAGB, RAGB, bA465E19.1
Description:Ras-related GTP binding B [Source:HGNC Symbol;Acc:19901]


Retrocopy-Parental alignment summary:






>retro_hsap_4
ATGCCAAATACAGCCATGAAGAAAAAGGTGCTGCTGATGGGGAAGAGCGGGTCGGGGAAGACCAGCATGAGGTCGATAAT
CTTCGCCAATTACATTGCTCGCGACACCCGGCGCCTGGGGGCCACCATTGACGTGGAACACTCCCACGTCCGATTCCTAG
GGAACCTGGTGCTGAACCTGTGGGACTGTGGCGGTCAGGACACCTTCATGGAAAATTACTTCACCAGCCAGCGAGACAAT
ATCTTCCGTAACGTGGAAGTTTTGATTTACGTGTTTGACGTGGAGAGCCGCGAACTGGAAAAGGACATGCATTATTACCA
GTCGTGTCTGGAGGCCATCCTCCAGAACTCTCCTGACGCCAAAATCTTCTGCCTGGTGCACAAAATGGATCTGGTTCAGG
AGGATCAGCGTGACCTGATTTTTAAAGAGCGAGAGGAAGACCTGAGGCGTCTGTCTCGCCCGCTGGAGTGTGCTTGTTTT
CGAACGTCCATCTGGGATGAGACGCTCTACAAAGCCTGGTCCAGCATCGTCTACCAGCTGATTCCCAACGTTCAGCAGCT
GGAGATGAACCTCAGGAATTTTGCCCAAATCATTGAGGCCGATGAAGTTCTGCTGTTCGAAAGAGCTACATTCTTGGTTA
TTTCCCACTACCAGTGCAAAGAGCAGCGCGACGTCCACCGGTTTGAGAAGATCAGCAACATCATCAAACAGTTCAAGCTG
AGCTGCAGTAAATTGGCCGCTTCCTTCCAGAGCATGGAAGTTAGGAATTCCAACTTCGCTGCTTTCATCGACATCTTCAC
CTCAAATACGTACGTGATGGTGGTCATGTCAGATCCGTCGATCCCTTCTGCGGCCACTCTGATCAACATTCGCAATGCCC
GGAAACACTTTGAGAAGCTGGAGAGAGTGGATGGCCCCAAGCACAGTCTCCTTATGCGTTGA

ORF - retro_hsap_4 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.08 %
Parental protein coverage: 90.46 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalLPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFM
.PNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFM
RetrocopyMPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFM
ParentalENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLI
ENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLI
RetrocopyENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLI
ParentalFKEREEDLRRLSRPLECSCFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAEIIEADEVLLFERAT
FKEREEDLRRLSRPLEC.CFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFA.IIEADEVLLFERAT
RetrocopyFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVLLFERAT
ParentalFLVISHYQCKEQRDAHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPS
FLVISHYQCKEQRD.HRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPS
RetrocopyFLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPS
ParentalIPSAATLINIRNARKHFEKLERVDGPKQCLLMR
IPSAATLINIRNARKHFEKLERVDGPK..LLMR
RetrocopyIPSAATLINIRNARKHFEKLERVDGPKHSLLMR

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 59 .14 RPM 7 .93 RPM
bodymap2_adrenal 50 .85 RPM 18 .89 RPM
bodymap2_brain 64 .04 RPM 30 .66 RPM
bodymap2_breast 47 .04 RPM 14 .30 RPM
bodymap2_colon 46 .48 RPM 16 .05 RPM
bodymap2_heart 38 .40 RPM 7 .02 RPM
bodymap2_kidney 49 .39 RPM 16 .98 RPM
bodymap2_liver 31 .20 RPM 3 .30 RPM
bodymap2_lung 39 .61 RPM 9 .92 RPM
bodymap2_lymph_node 43 .29 RPM 12 .35 RPM
bodymap2_ovary 66 .54 RPM 29 .65 RPM
bodymap2_prostate 58 .44 RPM 24 .53 RPM
bodymap2_skeletal_muscle 47 .91 RPM 6 .67 RPM
bodymap2_testis 50 .73 RPM 17 .21 RPM
bodymap2_thyroid 56 .85 RPM 36 .21 RPM
bodymap2_white_blood_cells 45 .14 RPM 5 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity may be related with retro_hsap_4 in 51 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 9:19049030..19049653
ENCFF002CFX POLR2A 9:19048972..19049663
ENCFF002CGN POLR2A 9:19049099..19049595
ENCFF002CHO POLR2A 9:19048883..19049876
ENCFF002CIH POLR2A 9:19049103..19049587
ENCFF002CIO POLR2A 9:19049051..19049635
ENCFF002CJE POLR2A 9:19048846..19049619
ENCFF002CJZ POLR2A 9:19048975..19049654
ENCFF002CKX POLR2A 9:19049090..19049631
ENCFF002CLM POLR2A 9:19049129..19049403
ENCFF002CMI POLR2A 9:19048967..19049671
ENCFF002COJ POLR2A 9:19049071..19049507
ENCFF002COJ POLR2A 9:19049271..19049707
ENCFF002CPG POLR2A 9:19049106..19049549
ENCFF002CPH POLR2A 9:19049066..19049456
ENCFF002CQA POLR2A 9:19049077..19049508
ENCFF002CQC POLR2A 9:19049075..19049647
ENCFF002CQE POLR2A 9:19049112..19049626
ENCFF002CQG POLR2A 9:19049099..19049618
ENCFF002CQI POLR2A 9:19049086..19049626
ENCFF002CQK POLR2A 9:19049017..19049668
ENCFF002CQM POLR2A 9:19049091..19049624
ENCFF002CQO POLR2A 9:19049051..19049660
ENCFF002CRK POLR2A 9:19049009..19049533
ENCFF002CRO POLR2A 9:19049144..19049355
ENCFF002CRO POLR2A 9:19049272..19049692
ENCFF002CSY POLR2A 9:19048909..19049727
ENCFF002CUP POLR2A 9:19049382..19049522
ENCFF002CUQ POLR2A 9:19049086..19049551
ENCFF002CVF POLR2A 9:19049141..19049376
ENCFF002CVJ POLR2A 9:19049042..19049672
ENCFF002CXM POLR2A 9:19049179..19049380
ENCFF002CXM POLR2A 9:19049236..19049726
ENCFF002CXN POLR2A 9:19049214..19049372
ENCFF002CXO POLR2A 9:19049161..19049364
ENCFF002CXO POLR2A 9:19049270..19049694
ENCFF002CXP POLR2A 9:19049119..19049532
ENCFF002CXR POLR2A 9:19049137..19049574
ENCFF002CZC POLR2A 9:19049018..19049667
ENCFF002CZD POLR2A 9:19049018..19049646
ENCFF002CZQ POLR2A 9:19049113..19049610
ENCFF002CZW POLR2A 9:19048922..19049718
ENCFF002CZY POLR2A 9:19049067..19049668
ENCFF002DAE POLR2A 9:19049144..19049377
ENCFF002DAH POLR2A 9:19049198..19049343
ENCFF002DAK POLR2A 9:19049171..19049355
ENCFF002DAS POLR2A 9:19049028..19049504
ENCFF002DAV POLR2A 9:19049134..19049438
ENCFF002DAV POLR2A 9:19049212..19049756
ENCFF002DAY POLR2A 9:19048965..19049601
ENCFF002DBB POLR2A 9:19049222..19049339
ENCFF002DBE POLR2A 9:19049095..19049431
ENCFF002DBO POLR2A 9:19049088..19049590
ENCFF002DBP POLR2A 9:19049111..19049407
ENCFF002DBQ POLR2A 9:19049140..19049393
ENCFF002DBT POLR2A 9:19049151..19049380

EST - click to see more details

14 EST(s) were mapped to retro_hsap_4 retrocopy
EST ID Start End Identity Match Mis-match Score
AA186991 19049678 19050166 95.1 477 7 458
AA310124 19049718 19050118 99.3 397 0 396
AA338377 19049913 19050292 97.9 378 1 374
BE081500 19049775 19050115 99.8 339 1 338
BF845083 19049822 19050157 100 335 0 335
BF914635 19049776 19050153 99.5 375 2 373
BG955634 19049794 19050228 98.9 428 5 422
BG986382 19049774 19050137 99.2 360 3 357
BG986383 19049765 19050136 99.2 366 2 361
BM313253 19049659 19050047 99 384 4 380
BP213970 19049679 19050176 99.2 492 4 488
CD688621 19049674 19050165 99.4 488 3 485
DN989399 19049641 19050144 100 502 0 501
F06456 19049756 19050107 99.8 345 1 344

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_1920575 libraries 0 libraries 0 libraries 4 libraries 1820 libraries

The graphical summary, for retro_hsap_4 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_4 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_48
Pongo abelii retro_pabe_191
Macaca mulatta retro_mmul_249
Callithrix jacchus retro_cjac_117
Mus musculus retro_mmus_159
Sus scrofa retro_sscr_15
Canis familiaris retro_cfam_421
Equus caballus retro_ecab_608
Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000129201 retrocopy
retro_amel_1842,
Canis familiaris ENSCAFG000000165031 retrocopy
retro_cfam_421,
Callithrix jacchus ENSCJAG000000073171 retrocopy
retro_cjac_117,
Cavia porcellus ENSCPOG000000112661 retrocopy
retro_cpor_86,
Equus caballus ENSECAG000000060201 retrocopy
retro_ecab_608,
Felis catus ENSFCAG000000139321 retrocopy
retro_fcat_21,
Homo sapiens ENSG00000083750 1 retrocopy
retro_hsap_4 ,
Gorilla gorilla ENSGGOG000000115011 retrocopy
retro_ggor_65,
Loxodonta africana ENSLAFG000000161441 retrocopy
retro_lafr_102,
Myotis lucifugus ENSMLUG000000157201 retrocopy
retro_mluc_40,
Macaca mulatta ENSMMUG000000176351 retrocopy
retro_mmul_249,
Mustela putorius furoENSMPUG000000037301 retrocopy
retro_mputfur_87,
Mus musculus ENSMUSG000000416581 retrocopy
retro_mmus_159,
Nomascus leucogenys ENSNLEG000000163501 retrocopy
retro_nleu_13,
Oryctolagus cuniculus ENSOCUG000000086661 retrocopy
retro_ocun_166,
Otolemur garnettii ENSOGAG000000003451 retrocopy
retro_ogar_675,
Procavia capensis ENSPCAG000000034171 retrocopy
retro_pcap_6,
Pongo abelii ENSPPYG000000203981 retrocopy
retro_pabe_191,
Pan troglodytes ENSPTRG000000219551 retrocopy
retro_ptro_48,
Rattus norvegicus ENSRNOG000000031601 retrocopy
retro_rnor_2,
Sus scrofa ENSSSCG000000298001 retrocopy
retro_sscr_15,

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 = 48.36 RPM Legend:


Library Retrogene expression
CEU_NA11831 41 .84 RPM
CEU_NA11843 37 .51 RPM
CEU_NA11930 35 .95 RPM
CEU_NA12004 43 .26 RPM
CEU_NA12400 42 .23 RPM
CEU_NA12751 35 .77 RPM
CEU_NA12760 42 .49 RPM
CEU_NA12827 34 .76 RPM
CEU_NA12872 36 .50 RPM
CEU_NA12873 37 .74 RPM
FIN_HG00183 31 .66 RPM
FIN_HG00277 42 .04 RPM
FIN_HG00315 40 .54 RPM
FIN_HG00321 37 .81 RPM
FIN_HG00328 39 .04 RPM
FIN_HG00338 48 .30 RPM
FIN_HG00349 40 .95 RPM
FIN_HG00375 40 .27 RPM
FIN_HG00377 39 .61 RPM
FIN_HG00378 43 .24 RPM
GBR_HG00099 47 .25 RPM
GBR_HG00111 39 .66 RPM
GBR_HG00114 42 .10 RPM
GBR_HG00119 33 .43 RPM
GBR_HG00131 40 .04 RPM
GBR_HG00133 41 .27 RPM
GBR_HG00134 38 .44 RPM
GBR_HG00137 45 .85 RPM
GBR_HG00142 31 .42 RPM
GBR_HG00143 44 .07 RPM
TSI_NA20512 45 .55 RPM
TSI_NA20513 44 .98 RPM
TSI_NA20518 43 .88 RPM
TSI_NA20532 36 .49 RPM
TSI_NA20538 36 .35 RPM
TSI_NA20756 46 .24 RPM
TSI_NA20765 34 .13 RPM
TSI_NA20771 39 .20 RPM
TSI_NA20786 47 .50 RPM
TSI_NA20798 44 .91 RPM
YRI_NA18870 42 .89 RPM
YRI_NA18907 47 .80 RPM
YRI_NA18916 37 .45 RPM
YRI_NA19093 48 .36 RPM
YRI_NA19099 47 .11 RPM
YRI_NA19114 37 .28 RPM
YRI_NA19118 38 .53 RPM
YRI_NA19213 38 .10 RPM
YRI_NA19214 43 .12 RPM
YRI_NA19223 39 .81 RPM

Indel association:

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



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