RetrogeneDB ID:

retro_hsap_3104

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:141287389..141288014(-)
Located in intron of:ENSG00000153130
Retrocopy
information
Ensembl ID:ENSG00000241923
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL14
Ensembl ID:ENSG00000188846
Aliases:RPL14, CAG-ISL-7, CTG-B33, L14, RL14, hRL14
Description:ribosomal protein L14 [Source:HGNC Symbol;Acc:10305]


Retrocopy-Parental alignment summary:






>retro_hsap_3104
ATGGTGTTCAGGCGCTTCGTGGAGGTTGGCCGTGTGGGCTACATCCCCTCTGGACCTCGTGCCAGAAAATTGGTTGCAAC
TGTAGATGTTATTGATCAAAACAGGGCTTTGGTTGATGGACCTTGCACTCAAGTGAGGAGACAGACCATGCCTTTCAAGT
GCATGCAGCTCACTGATTTCAACCTCAAGTTTCCACACAGAGCCCACCAGAAGTATGTCAGACAAGCCTGGCAGAAGGCA
AACATCAATACAAAATGGGCAGCCACACGATGGGCCAAGAAGATTGAAGCCAGAGAAAGGAAAGCCAAGATGACAGATTT
TGATCATTTTAAAGTTATGAAGGCAATGAGGAACAGAATAATCAAGAATGAAGTTAAGAAGCTTCAAAAGGCAGCTCTCC
AAAAGCTTCTCCCAAAAAAGCACCTGCTGCGAAGCGTGCTACTGCTGCTGCAGCTGCTGCTAAAGTTCTAGCAAAAAGAT
GACCGCTGCAGGCAAGAAGGCTCCAGCTTAGAAGCTTCCTGCCCAGAAAGCCACAGGCCAGAAGGCAGCGCCTCCTCCAA
AAGCTCAGAAGGGTCAAAAAGCTCCAGCCCAGAAAGCACCTGCTCCAAAAGCGTTTGGCAAGAAA

ORF - retro_hsap_3104 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.65 %
Parental protein coverage: 99.53 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMPFKCMQLTDFILKFPHSAHQ
MVFRRFVEVGRV.Y...GP.A.KLVA.VDVIDQNRALVDGPCTQVRRQ.MPFKCMQLTDF.LKFPH.AHQ
RetrocopyMVFRRFVEVGRVGYIPSGPRARKLVATVDVIDQNRALVDGPCTQVRRQTMPFKCMQLTDFNLKFPHRAHQ
ParentalKYVRQAWQKADINTKWAATRWAKKIEARERKAKMTDFDRFKVMKAKKMRNRIIKNEVKKLQKAALL-KAS
KYVRQAWQKA.INTKWAATRWAKKIEARERKAKMTDFD.FKVMKA..MRNRIIKNEVKKLQKAAL..KAS
RetrocopyKYVRQAWQKANINTKWAATRWAKKIEARERKAKMTDFDHFKVMKA--MRNRIIKNEVKKLQKAALQ<KAS
ParentalPKKAPGTKGTAAAAAAAAAAKVPA-KKITAASKKAPAQKVPAQKATGQKAAPAPKAQKGQKAPAQKAPAP
PKKAP..K....A.AAAAAAKV.A.KK.TAA.KKAPA.K.PAQKATGQKAAP.PKAQKGQKAPAQKAPAP
RetrocopyPKKAPAAK---RATAAAAAAKVLA<KKMTAAGKKAPA*KLPAQKATGQKAAPPPKAQKGQKAPAQKAPAP
ParentalKASGKK
KA.GKK
RetrocopyKAFGKK

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 .00 RPM 299 .14 RPM
bodymap2_adrenal 0 .06 RPM 319 .71 RPM
bodymap2_brain 0 .07 RPM 97 .58 RPM
bodymap2_breast 0 .00 RPM 176 .29 RPM
bodymap2_colon 0 .00 RPM 355 .99 RPM
bodymap2_heart 0 .07 RPM 110 .66 RPM
bodymap2_kidney 0 .12 RPM 152 .44 RPM
bodymap2_liver 0 .17 RPM 121 .02 RPM
bodymap2_lung 0 .02 RPM 333 .16 RPM
bodymap2_lymph_node 0 .11 RPM 354 .64 RPM
bodymap2_ovary 0 .04 RPM 392 .07 RPM
bodymap2_prostate 0 .05 RPM 571 .10 RPM
bodymap2_skeletal_muscle 0 .25 RPM 267 .83 RPM
bodymap2_testis 0 .23 RPM 185 .40 RPM
bodymap2_thyroid 0 .21 RPM 182 .08 RPM
bodymap2_white_blood_cells 0 .02 RPM 460 .64 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3104 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3104 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_14008095 libraries36 libraries313 libraries480 libraries905 libraries

The graphical summary, for retro_hsap_3104 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_3104 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3104 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2100
Callithrix jacchus retro_cjac_2139
Parental genes homology:
Parental genes homology involve 26 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017094 retrocopies
retro_amel_1876, retro_amel_1933, retro_amel_296, retro_amel_660,
Canis familiaris ENSCAFG000000051381 retrocopy
retro_cfam_31,
Callithrix jacchus ENSCJAG000000178849 retrocopies
retro_cjac_1249, retro_cjac_1393, retro_cjac_1835, retro_cjac_2138, retro_cjac_2139, retro_cjac_2332, retro_cjac_2797, retro_cjac_3240, retro_cjac_630,
Cavia porcellus ENSCPOG000000007111 retrocopy
retro_cpor_529,
Equus caballus ENSECAG000000268132 retrocopies
retro_ecab_377, retro_ecab_743,
Echinops telfairi ENSETEG000000128946 retrocopies
retro_etel_2117, retro_etel_2155, retro_etel_251, retro_etel_315, retro_etel_356, retro_etel_387,
Felis catus ENSFCAG000000156554 retrocopies
retro_fcat_1000, retro_fcat_1457, retro_fcat_587, retro_fcat_671,
Homo sapiens ENSG00000188846 6 retrocopies
retro_hsap_1015, retro_hsap_1047, retro_hsap_2796, retro_hsap_3104 , retro_hsap_3352, retro_hsap_4777,
Gorilla gorilla ENSGGOG000000259583 retrocopies
retro_ggor_122, retro_ggor_1945, retro_ggor_2272,
Latimeria chalumnae ENSLACG000000156391 retrocopy
retro_lcha_29,
Microcebus murinus ENSMICG000000092174 retrocopies
retro_mmur_1218, retro_mmur_1352, retro_mmur_279, retro_mmur_3,
Myotis lucifugus ENSMLUG000000144294 retrocopies
retro_mluc_1294, retro_mluc_2263, retro_mluc_420, retro_mluc_563,
Monodelphis domestica ENSMODG000000152622 retrocopies
retro_mdom_1499, retro_mdom_1939,
Mustela putorius furoENSMPUG000000179611 retrocopy
retro_mputfur_90,
Mus musculus ENSMUSG000000257943 retrocopies
retro_mmus_2904, retro_mmus_2929, retro_mmus_3011,
Nomascus leucogenys ENSNLEG000000056822 retrocopies
retro_nleu_763, retro_nleu_918,
Oryctolagus cuniculus ENSOCUG000000103093 retrocopies
retro_ocun_410, retro_ocun_464, retro_ocun_656,
Pan troglodytes ENSPTRG000000119634 retrocopies
retro_ptro_1893, retro_ptro_2100, retro_ptro_2135, retro_ptro_713,
Pteropus vampyrus ENSPVAG000000139147 retrocopies
retro_pvam_1108, retro_pvam_1413, retro_pvam_246, retro_pvam_446, retro_pvam_683, retro_pvam_903, retro_pvam_904,
Rattus norvegicus ENSRNOG000000190074 retrocopies
retro_rnor_2268, retro_rnor_2620, retro_rnor_415, retro_rnor_591,
Sorex araneus ENSSARG000000039742 retrocopies
retro_sara_349, retro_sara_504,
Sarcophilus harrisii ENSSHAG000000015915 retrocopies
retro_shar_397, retro_shar_539, retro_shar_696, retro_shar_737, retro_shar_788,
Sus scrofa ENSSSCG000000112722 retrocopies
retro_sscr_521, retro_sscr_63,
Tarsius syrichta ENSTSYG000000021615 retrocopies
retro_tsyr_1036, retro_tsyr_1404, retro_tsyr_176, retro_tsyr_361, retro_tsyr_956,
Tursiops truncatus ENSTTRG000000067081 retrocopy
retro_ttru_113,
Xenopus tropicalis ENSXETG000000220181 retrocopy
retro_xtro_3,

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 = 0.77 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .30 RPM
CEU_NA11843 0 .57 RPM
CEU_NA11930 0 .26 RPM
CEU_NA12004 0 .57 RPM
CEU_NA12400 0 .32 RPM
CEU_NA12751 0 .44 RPM
CEU_NA12760 0 .27 RPM
CEU_NA12827 0 .33 RPM
CEU_NA12872 0 .35 RPM
CEU_NA12873 0 .26 RPM
FIN_HG00183 0 .33 RPM
FIN_HG00277 0 .44 RPM
FIN_HG00315 0 .52 RPM
FIN_HG00321 0 .27 RPM
FIN_HG00328 0 .40 RPM
FIN_HG00338 0 .62 RPM
FIN_HG00349 0 .77 RPM
FIN_HG00375 0 .54 RPM
FIN_HG00377 0 .35 RPM
FIN_HG00378 0 .15 RPM
GBR_HG00099 0 .55 RPM
GBR_HG00111 0 .58 RPM
GBR_HG00114 0 .34 RPM
GBR_HG00119 0 .17 RPM
GBR_HG00131 0 .29 RPM
GBR_HG00133 0 .19 RPM
GBR_HG00134 0 .24 RPM
GBR_HG00137 0 .33 RPM
GBR_HG00142 0 .44 RPM
GBR_HG00143 0 .26 RPM
TSI_NA20512 0 .20 RPM
TSI_NA20513 0 .41 RPM
TSI_NA20518 0 .58 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .51 RPM
TSI_NA20756 0 .20 RPM
TSI_NA20765 0 .31 RPM
TSI_NA20771 0 .51 RPM
TSI_NA20786 0 .24 RPM
TSI_NA20798 0 .25 RPM
YRI_NA18870 0 .44 RPM
YRI_NA18907 0 .31 RPM
YRI_NA18916 0 .34 RPM
YRI_NA19093 0 .21 RPM
YRI_NA19099 0 .40 RPM
YRI_NA19114 0 .31 RPM
YRI_NA19118 0 .25 RPM
YRI_NA19213 0 .38 RPM
YRI_NA19214 0 .49 RPM
YRI_NA19223 0 .28 RPM

Indel association:

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





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