RetrogeneDB ID:

retro_hsap_4677

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:40767239..40767641(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000189145
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL32
Ensembl ID:ENSG00000144713
Aliases:RPL32, L32
Description:ribosomal protein L32 [Source:HGNC Symbol;Acc:10336]


Retrocopy-Parental alignment summary:






>retro_hsap_4677
GCTGCCCTCAGACCCCTTGTGAAACTCAAGATTGTCAAAAAGAGAACCAAGAAGTTCATCCTGTACCAGTCAGACTGGTA
TGTCAAAATCAAGCCTAACTGGCAGAAACCCAGAGGTATTGACAATAGGGTTTGTAGAAGGTTCAAGGGCCAGATCTTGA
AGCCCATCGTTGGTTATGGGAGCAACAAAAAAACAAAGCACATGCTGCCCAATGGTTTCCGGAAATTCCTGGTCCATGAC
ATCAATGAGCTGGAAGTGCTGATGATGTGCAACAAATCTTACTGTGCTAAGATCGCTCACAATGTTTCCTCCAAGAACTG
CAAGGCCATCGTGGAAAGAGCAGCCCAGCTGGCCATCAGAGTCAACAACCTCAATGCCATACTGCGCAGCAAAGAAAATG
AA

ORF - retro_hsap_4677 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.33 %
Parental protein coverage: 99.26 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHMLP
AALRPLVK.KIVKKRTKKFI..QSD.YVKIK.NW.KPRGIDNRV.RRFKGQIL.P..GYGSNKKTKHMLP
RetrocopyAALRPLVKLKIVKKRTKKFILYQSDWYVKIKPNWQKPRGIDNRVCRRFKGQILKPIVGYGSNKKTKHMLP
ParentalSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEENE
.GFRKFLVH...ELEVL.MCNKSYCA.IAHNVSSKN.KAIVERAAQLAIRV.N.NA.LRS.ENE
RetrocopyNGFRKFLVHDINELEVLMMCNKSYCAKIAHNVSSKNCKAIVERAAQLAIRVNNLNAILRSKENE

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 475 .56 RPM
bodymap2_adrenal 0 .00 RPM 645 .14 RPM
bodymap2_brain 0 .00 RPM 173 .69 RPM
bodymap2_breast 0 .00 RPM 411 .62 RPM
bodymap2_colon 0 .00 RPM 532 .72 RPM
bodymap2_heart 0 .00 RPM 193 .31 RPM
bodymap2_kidney 0 .00 RPM 252 .38 RPM
bodymap2_liver 0 .00 RPM 251 .27 RPM
bodymap2_lung 0 .00 RPM 695 .97 RPM
bodymap2_lymph_node 0 .00 RPM 911 .91 RPM
bodymap2_ovary 0 .00 RPM 690 .71 RPM
bodymap2_prostate 0 .00 RPM 978 .90 RPM
bodymap2_skeletal_muscle 0 .00 RPM 881 .20 RPM
bodymap2_testis 0 .00 RPM 384 .92 RPM
bodymap2_thyroid 0 .00 RPM 314 .29 RPM
bodymap2_white_blood_cells 0 .00 RPM 1080 .68 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4677 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4677 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_19958881 libraries40 libraries796 libraries548 libraries364 libraries

The graphical summary, for retro_hsap_4677 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_4677 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4677 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 13 parental genes, and 103 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000147633 retrocopies
retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca ENSAMEG0000000458326 retrocopies
retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Cavia porcellus ENSCPOG000000199672 retrocopies
retro_cpor_1241, retro_cpor_608,
Dipodomys ordii ENSDORG000000084266 retrocopies
retro_dord_175, retro_dord_251, retro_dord_371, retro_dord_458, retro_dord_522, retro_dord_664,
Equus caballus ENSECAG000000072014 retrocopies
retro_ecab_1115, retro_ecab_26, retro_ecab_369, retro_ecab_698,
Erinaceus europaeus ENSEEUG000000116095 retrocopies
retro_eeur_161, retro_eeur_247, retro_eeur_300, retro_eeur_39, retro_eeur_576,
Homo sapiens ENSG00000144713 20 retrocopies
retro_hsap_1013, retro_hsap_1115, retro_hsap_1547, retro_hsap_1789, retro_hsap_1956, retro_hsap_2618, retro_hsap_2821, retro_hsap_2891, retro_hsap_3024, retro_hsap_3450, retro_hsap_3536, retro_hsap_3582, retro_hsap_3726, retro_hsap_3805, retro_hsap_3936, retro_hsap_3982, retro_hsap_4008, retro_hsap_4155, retro_hsap_4677 , retro_hsap_814,
Loxodonta africana ENSLAFG000000327371 retrocopy
retro_lafr_14,
Myotis lucifugus ENSMLUG000000225286 retrocopies
retro_mluc_100, retro_mluc_1283, retro_mluc_173, retro_mluc_2224, retro_mluc_2256, retro_mluc_48,
Mus musculus ENSMUSG0000005784116 retrocopies
retro_mmus_1132, retro_mmus_1142, retro_mmus_1746, retro_mmus_2010, retro_mmus_2263, retro_mmus_2316, retro_mmus_2341, retro_mmus_2699, retro_mmus_3099, retro_mmus_3378, retro_mmus_3605, retro_mmus_385, retro_mmus_442, retro_mmus_496, retro_mmus_533, retro_mmus_985,
Rattus norvegicus ENSRNOG000000107464 retrocopies
retro_rnor_179, retro_rnor_27, retro_rnor_278, retro_rnor_327,
Sarcophilus harrisii ENSSHAG000000127821 retrocopy
retro_shar_580,
Ictidomys tridecemlineatus ENSSTOG000000265059 retrocopies
retro_itri_1294, retro_itri_1322, retro_itri_1465, retro_itri_1639, retro_itri_1715, retro_itri_1748, retro_itri_370, retro_itri_885, retro_itri_948,

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 ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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





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