RetrogeneDB ID:

retro_hsap_4229

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:7477042..7478320(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230207
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL4
Ensembl ID:ENSG00000174444
Aliases:RPL4, L4
Description:ribosomal protein L4 [Source:HGNC Symbol;Acc:10353]


Retrocopy-Parental alignment summary:






>retro_hsap_4229
ATGGCGTGTGTCCGCCCACTGATGTCGCTGTACTCCGAAAAGGGGGAGTCATCTGGCAAAAATGTCACTTAGCCCGCTGT
ATTCAAGGCTCCTATTCGACCAGACATCGTGAACTTTGTTCACACCAACTTGCGCAAAAACAACAGACAGCCCTACGCTG
CCAGTGAATTAGCAGGTCATCGGACCAGCACTGAGTCTTGGGGTACTGGCAGAGCTGTGGCTCGAATTCCCAGAGTTCGA
GGTGGTGGGACTCACCGCTCCGGCCAGGGTGCTTTTGGAAACATGTGTCGTGGAGGCCGAAGGTTTGCACCAACCAAAAC
CTGGCGCCGTTGGCATCGTAGAGTGAACACAACCCAAAAACGGTATGCCATCTGTTCTGCCCTGGCTGCCTCAGCCCTAC
CAGCACTGGTCATGTCTAAAGGTCATCGTATTGAGGAAGTTCCTGAACTTCCTTTGGTAGTCGAAGATAAAGTTGAAGGC
TACAGGAAGACCAAGGAAGCTGTTTTGCTCCTTAAGAAACTTAAAGCCAGGAACGATATCAAAAAGGTCTATGCCTCTCA
GCGAATGAGAGCTGGCAAAGGCAAAATGAGAAACCGTCGCCGTATCCAGCGCAGGGGCCCGTGCATCATCTATAATGAGG
ATAATGGTATCAAGGCCTTCAGAAACATCCCTGCAATTACTCTGCTTAATGTAAGCAAGCTGACCATTTCGAAGCTTGCT
CCTGGTGGGCACGTGGGACGTTTCTGCATTTGGACTGGAAGTGCTTTCCGGAAGTTGGATGAATTGTATGGCACTTGGCG
TAAAGCCGCTTCCCTCAAGAGTAACTACAATCTTCCCATGCACAAGATGATTAATACAGATCTTAGCAGAATCTTGAAAA
GCCCAGAGATCCAAAGAGCCTTTCGGGCACCAAGCAAGAAGATTCATCGCAGAGTCCTAAAGAAGAACCCACTGAAAAAC
TTGAGAATCATGTTGAAGCTAAACCCATATGCAAAGACCATGCGCCGGAACACCATTCTTCGCCAGGCCAGGAATCACAA
GCTCCGGATGGATAAGGCAGCTGCTGCTGCAGCAGCACTAGAAGCCAAACCAGATGAGAAGGCGGCGGTTGCAGGCAAGA
AGCCTGTGGTAGGTAAGAAAGGAAAGAAGGCTGCTGTTGGTGTGAAGAAGCAGAAGAAGCCTCTGGTGGGAAAAAAGGCA
GCAGCTACCAAGAAATCAGCCCCTGAAAAGAAGCCTGCAGAAAAGAAACCTACTGTAGAGGAAAAGAAGCCTGCTGCA

ORF - retro_hsap_4229 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.85 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTG
MAC.RPL.S.YSEKGESSGKNVT.PAVFKAPIRPDIVNFVHTNLRKNNRQPYA.SELAGH.TS.ESWGTG
RetrocopyMACVRPLMSLYSEKGESSGKNVT*PAVFKAPIRPDIVNFVHTNLRKNNRQPYAASELAGHRTSTESWGTG
ParentalRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSK
RAVARIPRVRGGGTHRSGQGAFGNMCRGGR.FAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSK
RetrocopyRAVARIPRVRGGGTHRSGQGAFGNMCRGGRRFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSK
ParentalGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRGPCII
GHRIEEVPELPLVVEDKVEGY.KTKEAVLLLKKLKA.NDIKKVYASQRMRAGKGKMRNRRRIQRRGPCII
RetrocopyGHRIEEVPELPLVVEDKVEGYRKTKEAVLLLKKLKARNDIKKVYASQRMRAGKGKMRNRRRIQRRGPCII
ParentalYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLP
YNEDNG.IKAFRNIP.ITLLNVSKL.I.KLAPGGHVGRFCIWT.SAFRKLDELYGTWRKAASLKSNYNLP
RetrocopyYNEDNG-IKAFRNIPAITLLNVSKLTISKLAPGGHVGRFCIWTGSAFRKLDELYGTWRKAASLKSNYNLP
ParentalMHKMINTDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLR
MHKMINTDLSRILKSPEIQRA.RAP.KKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLR
RetrocopyMHKMINTDLSRILKSPEIQRAFRAPSKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLR
ParentalVDKAAAAAAALQAKSDEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKKPAPEKKPAEKKPTT
.DKAAAAAAAL.AK.DEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKK.APEKKPAEKKPT.
RetrocopyMDKAAAAAAALEAKPDEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKKSAPEKKPAEKKPTV
ParentalEEKKPAA
EEKKPAA
RetrocopyEEKKPAA

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 .60 RPM 1176 .34 RPM
bodymap2_adrenal 1 .11 RPM 1315 .18 RPM
bodymap2_brain 0 .07 RPM 413 .34 RPM
bodymap2_breast 1 .01 RPM 811 .84 RPM
bodymap2_colon 1 .26 RPM 1426 .23 RPM
bodymap2_heart 0 .13 RPM 355 .04 RPM
bodymap2_kidney 0 .27 RPM 476 .37 RPM
bodymap2_liver 0 .08 RPM 408 .55 RPM
bodymap2_lung 0 .30 RPM 1008 .37 RPM
bodymap2_lymph_node 0 .44 RPM 1227 .00 RPM
bodymap2_ovary 1 .21 RPM 1731 .25 RPM
bodymap2_prostate 1 .06 RPM 1700 .57 RPM
bodymap2_skeletal_muscle 0 .35 RPM 932 .47 RPM
bodymap2_testis 0 .57 RPM 864 .75 RPM
bodymap2_thyroid 0 .68 RPM 937 .95 RPM
bodymap2_white_blood_cells 0 .47 RPM 1745 .21 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_4229 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4229 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_193936392 libraries 514 libraries 903 libraries 20 libraries 0 libraries

The graphical summary, for retro_hsap_4229 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_4229 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4229 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2873
Gorilla gorilla retro_ggor_2831
Parental genes homology:
Parental genes homology involve 27 parental genes, and 105 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000052112 retrocopies
retro_btau_101, retro_btau_610,
Canis familiaris ENSCAFG000000173091 retrocopy
retro_cfam_72,
Choloepus hoffmanni ENSCHOG000000030086 retrocopies
retro_chof_1014, retro_chof_1496, retro_chof_2219, retro_chof_2616, retro_chof_455, retro_chof_476,
Callithrix jacchus ENSCJAG000000074912 retrocopies
retro_cjac_251, retro_cjac_945,
Dasypus novemcinctus ENSDNOG000000066933 retrocopies
retro_dnov_1028, retro_dnov_1152, retro_dnov_1931,
Equus caballus ENSECAG000000231791 retrocopy
retro_ecab_428,
Echinops telfairi ENSETEG000000003373 retrocopies
retro_etel_1876, retro_etel_2195, retro_etel_226,
Felis catus ENSFCAG000000122934 retrocopies
retro_fcat_1136, retro_fcat_189, retro_fcat_505, retro_fcat_567,
Homo sapiens ENSG00000174444 5 retrocopies
retro_hsap_1306, retro_hsap_254, retro_hsap_2898, retro_hsap_4229 , retro_hsap_471,
Gorilla gorilla ENSGGOG000000036954 retrocopies
retro_ggor_1023, retro_ggor_2008, retro_ggor_2831, retro_ggor_304,
Loxodonta africana ENSLAFG000000064943 retrocopies
retro_lafr_1076, retro_lafr_152, retro_lafr_960,
Microcebus murinus ENSMICG000000044196 retrocopies
retro_mmur_1050, retro_mmur_1330, retro_mmur_440, retro_mmur_562, retro_mmur_830, retro_mmur_852,
Myotis lucifugus ENSMLUG000000118092 retrocopies
retro_mluc_121, retro_mluc_198,
Macaca mulatta ENSMMUG000000168442 retrocopies
retro_mmul_2160, retro_mmul_649,
Monodelphis domestica ENSMODG000000096572 retrocopies
retro_mdom_656, retro_mdom_944,
Mustela putorius furoENSMPUG000000003373 retrocopies
retro_mputfur_1205, retro_mputfur_411, retro_mputfur_570,
Nomascus leucogenys ENSNLEG000000129384 retrocopies
retro_nleu_1041, retro_nleu_1062, retro_nleu_2385, retro_nleu_887,
Pongo abelii ENSPPYG000000065781 retrocopy
retro_pabe_152,
Pan troglodytes ENSPTRG000000071956 retrocopies
retro_ptro_1512, retro_ptro_1959, retro_ptro_214, retro_ptro_2873, retro_ptro_353, retro_ptro_897,
Pteropus vampyrus ENSPVAG0000000006818 retrocopies
retro_pvam_1222, retro_pvam_1342, retro_pvam_201, retro_pvam_202, retro_pvam_216, retro_pvam_236, retro_pvam_267, retro_pvam_399, retro_pvam_428, retro_pvam_430, retro_pvam_435, retro_pvam_466, retro_pvam_518, retro_pvam_736, retro_pvam_778, retro_pvam_819, retro_pvam_865, retro_pvam_955,
Rattus norvegicus ENSRNOG000000093785 retrocopies
retro_rnor_1192, retro_rnor_1621, retro_rnor_2061, retro_rnor_2484, retro_rnor_949,
Sus scrofa ENSSSCG000000049452 retrocopies
retro_sscr_138, retro_sscr_885,
Ictidomys tridecemlineatus ENSSTOG000000092211 retrocopy
retro_itri_437,
Tupaia belangeri ENSTBEG000000143929 retrocopies
retro_tbel_1701, retro_tbel_2186, retro_tbel_2649, retro_tbel_3302, retro_tbel_3577, retro_tbel_3624, retro_tbel_3938, retro_tbel_4340, retro_tbel_4402,
Tarsius syrichta ENSTSYG000000055881 retrocopy
retro_tsyr_1144,
Tursiops truncatus ENSTTRG000000102067 retrocopies
retro_ttru_1130, retro_ttru_1399, retro_ttru_1713, retro_ttru_177, retro_ttru_789, retro_ttru_817, retro_ttru_964,
Vicugna pacos ENSVPAG000000067462 retrocopies
retro_vpac_143, retro_vpac_250,

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 = 2.18 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .03 RPM
CEU_NA11843 1 .62 RPM
CEU_NA11930 2 .18 RPM
CEU_NA12004 1 .44 RPM
CEU_NA12400 0 .95 RPM
CEU_NA12751 1 .04 RPM
CEU_NA12760 1 .48 RPM
CEU_NA12827 0 .94 RPM
CEU_NA12872 1 .09 RPM
CEU_NA12873 0 .80 RPM
FIN_HG00183 1 .35 RPM
FIN_HG00277 0 .85 RPM
FIN_HG00315 1 .32 RPM
FIN_HG00321 1 .45 RPM
FIN_HG00328 1 .07 RPM
FIN_HG00338 1 .17 RPM
FIN_HG00349 1 .59 RPM
FIN_HG00375 1 .32 RPM
FIN_HG00377 1 .19 RPM
FIN_HG00378 0 .72 RPM
GBR_HG00099 1 .54 RPM
GBR_HG00111 0 .97 RPM
GBR_HG00114 0 .92 RPM
GBR_HG00119 1 .03 RPM
GBR_HG00131 0 .86 RPM
GBR_HG00133 0 .84 RPM
GBR_HG00134 0 .61 RPM
GBR_HG00137 0 .91 RPM
GBR_HG00142 1 .03 RPM
GBR_HG00143 0 .86 RPM
TSI_NA20512 0 .93 RPM
TSI_NA20513 0 .97 RPM
TSI_NA20518 1 .80 RPM
TSI_NA20532 0 .75 RPM
TSI_NA20538 1 .34 RPM
TSI_NA20756 1 .72 RPM
TSI_NA20765 0 .75 RPM
TSI_NA20771 1 .87 RPM
TSI_NA20786 0 .94 RPM
TSI_NA20798 0 .50 RPM
YRI_NA18870 1 .29 RPM
YRI_NA18907 0 .83 RPM
YRI_NA18916 0 .82 RPM
YRI_NA19093 0 .62 RPM
YRI_NA19099 1 .22 RPM
YRI_NA19114 0 .92 RPM
YRI_NA19118 0 .95 RPM
YRI_NA19213 1 .20 RPM
YRI_NA19214 0 .74 RPM
YRI_NA19223 0 .70 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017