RetrogeneDB ID:

retro_hsap_3353

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:86180048..86180698(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000242477
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL10A
Ensembl ID:ENSG00000198755
Aliases:RPL10A, CSA19, Csa-19, L10A, NEDD6
Description:ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]


Retrocopy-Parental alignment summary:






>retro_hsap_3353
ATGAGCAGCAAAGTCTCTCGCGACACCCAGTGGGAGGCAGTGCGGAAAGTCCTGCACAGGAACCAGCGCTAGCGCCACAA
ATTCCAGGAGACGGTGTAGGTGCAGATCAGCTTGAAGAAGTATGACCCACAGAAGGACAAGTGCTCCTCGGGCACCATCA
GGCTTAAGTCCACTCCCCGCCCCAAGTTCTCTGTGTGTGTTCTGGCGGACCAGTAGCACTGCGACGAGGCCAAGGCCATG
GATATCCCCCACATGGACACTGAGGCGCTGAAAAAACTCAACAAGAATAAAAAACTGGTCAAGAAGCTGGCCAAGAAGTA
TGATGCGTTTTTGGCCTCAGAGTCTCTGATCAAGCAGATTCCACGAATCCTCGGCCCAGATCTAAATAAGGCAGGAAAGT
TCCCTTCCCTGCTCACACACAACGAAAACATGGTGGCCAAAGTGGATGAGGTGAAGTTCACAATCAAGTTCCAAATGAAG
AAGGTGTTATATCTGGCTGTAGCTGTTGGTCACGTGAAGATGACAGACGATGAGCTTGTGGATAACATTCACCTGGCTGT
CAGCTTCTTGTTGTCATTGCTCAAGAAATACTGGCAGAATGTCCGGCCTTATATATCAAGAGCACCATGGGCAAGCCCCA
GCGCCTATAT

ORF - retro_hsap_3353 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.53 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 3
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGD
MSSKVSRDT..EAVR.VLH.NQR.R.KF.ETV..QISLK.YDPQKDK..SGT.RLKSTPRPKFSVCVL.D
RetrocopyMSSKVSRDTQWEAVRKVLHRNQR*RHKFQETV*VQISLKKYDPQKDKCSSGTIRLKSTPRPKFSVCVLAD
ParentalQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTH
Q.HCDEAKA.DIPHMD.EALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGP.LNKAGKFPSLLTH
RetrocopyQ*HCDEAKAMDIPHMDTEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPDLNKAGKFPSLLTH
ParentalNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVR-ALYIKST
NENMVAKVDEVK.TIKFQMKKVL.LAVAVGHVKMTDDELV.NIHLAV.FL.SLLKK.WQNVR.ALYIKST
RetrocopyNENMVAKVDEVKFTIKFQMKKVLYLAVAVGHVKMTDDELVDNIHLAVSFLLSLLKKYWQNVR<ALYIKST
ParentalMGKPQRLY
MGKPQRLY
RetrocopyMGKPQRLY

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 .02 RPM 373 .55 RPM
bodymap2_adrenal 0 .12 RPM 462 .34 RPM
bodymap2_brain 0 .02 RPM 118 .86 RPM
bodymap2_breast 0 .02 RPM 239 .75 RPM
bodymap2_colon 0 .02 RPM 606 .18 RPM
bodymap2_heart 0 .02 RPM 119 .96 RPM
bodymap2_kidney 0 .02 RPM 264 .71 RPM
bodymap2_liver 0 .00 RPM 193 .24 RPM
bodymap2_lung 0 .04 RPM 499 .54 RPM
bodymap2_lymph_node 0 .15 RPM 511 .32 RPM
bodymap2_ovary 0 .04 RPM 813 .85 RPM
bodymap2_prostate 0 .03 RPM 994 .59 RPM
bodymap2_skeletal_muscle 0 .20 RPM 389 .84 RPM
bodymap2_testis 0 .02 RPM 250 .35 RPM
bodymap2_thyroid 0 .04 RPM 301 .21 RPM
bodymap2_white_blood_cells 0 .00 RPM 605 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_3353 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3353 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_156397119 libraries 83 libraries 763 libraries 651 libraries 213 libraries

The graphical summary, for retro_hsap_3353 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_3353 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3353 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2273
Parental genes homology:
Parental genes homology involve 14 parental genes, and 86 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000067013 retrocopies
retro_amel_1144, retro_amel_1223, retro_amel_1262, retro_amel_1591, retro_amel_1813, retro_amel_198, retro_amel_318, retro_amel_320, retro_amel_417, retro_amel_520, retro_amel_609, retro_amel_710, retro_amel_970,
Echinops telfairi ENSETEG000000133252 retrocopies
retro_etel_1974, retro_etel_326,
Felis catus ENSFCAG000000129047 retrocopies
retro_fcat_1144, retro_fcat_1488, retro_fcat_1561, retro_fcat_1971, retro_fcat_210, retro_fcat_262, retro_fcat_560,
Homo sapiens ENSG00000198755 13 retrocopies
retro_hsap_142, retro_hsap_1462, retro_hsap_1710, retro_hsap_177, retro_hsap_1935, retro_hsap_2795, retro_hsap_3025, retro_hsap_3245, retro_hsap_3353 , retro_hsap_337, retro_hsap_3949, retro_hsap_4025, retro_hsap_4040,
Gorilla gorilla ENSGGOG0000002814010 retrocopies
retro_ggor_1, retro_ggor_1124, retro_ggor_1282, retro_ggor_1407, retro_ggor_2088, retro_ggor_2273, retro_ggor_234, retro_ggor_2702, retro_ggor_358, retro_ggor_57,
Macropus eugenii ENSMEUG000000057606 retrocopies
retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Macaca mulatta ENSMMUG000000159076 retrocopies
retro_mmul_1931, retro_mmul_2041, retro_mmul_2321, retro_mmul_2330, retro_mmul_306, retro_mmul_583,
Monodelphis domestica ENSMODG000000137662 retrocopies
retro_mdom_276, retro_mdom_499,
Nomascus leucogenys ENSNLEG0000000865013 retrocopies
retro_nleu_1174, retro_nleu_1210, retro_nleu_1697, retro_nleu_1778, retro_nleu_1980, retro_nleu_2055, retro_nleu_2342, retro_nleu_2436, retro_nleu_2879, retro_nleu_662, retro_nleu_838, retro_nleu_986, retro_nleu_989,
Ornithorhynchus anatinus ENSOANG000000145741 retrocopy
retro_oana_86,
Oryctolagus cuniculus ENSOCUG000000040652 retrocopies
retro_ocun_130, retro_ocun_4,
Rattus norvegicus ENSRNOG000000005054 retrocopies
retro_rnor_2302, retro_rnor_37, retro_rnor_400, retro_rnor_43,
Sarcophilus harrisii ENSSHAG000000020471 retrocopy
retro_shar_438,
Tursiops truncatus ENSTTRG000000094316 retrocopies
retro_ttru_100, retro_ttru_1137, retro_ttru_1325, retro_ttru_1477, retro_ttru_205, retro_ttru_494,

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 = 0.36 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .16 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .36 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .12 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .17 RPM
FIN_HG00375 0 .10 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .19 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .20 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .08 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .14 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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