RetrogeneDB ID:

retro_hsap_1345

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:59261396..59261744(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213598
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL31
Ensembl ID:ENSG00000071082
Aliases:RPL31, L31
Description:ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]


Retrocopy-Parental alignment summary:






>retro_hsap_1345
AGAAGAAAACGGGCCGTTGCCATCAACGAAGTGGTAACCCGAGAATATACCATCAACATTCACAAGCGCATCCATGGAGT
GGGCTTCAAGAAACGTGCACCTTGGGCACTCAAAGAGATTCGGAAATTTGCCATGAAGGAGATGGGAACTCCAGATGTGC
GCATTGACACCAGGCTCAACAAAGCTGTCTGGGCCAAAGGAATAAGGAATGTCCTATACCGAATCCATGTGAGGCTGTCC
AGAAAACGTAATGAGGATGAAGATTCACCAAATAAGCTATATACTTTGGTTACCTATGTAACTGTTACCACTTTCAAAAA
TCTACAGACAGTCAATGTGGATGAGAAC

ORF - retro_hsap_1345 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.24 %
Parental protein coverage: 92.8 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKKKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVWAKGIRN
..K...AINEVVTREYTINIHKRIHGVGFKKRAP.ALKEIRKFAMKEMGTPDVRIDTRLNKAVWAKGIRN
RetrocopyRRKRAVAINEVVTREYTINIHKRIHGVGFKKRAPWALKEIRKFAMKEMGTPDVRIDTRLNKAVWAKGIRN
ParentalVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQTVNVDEN
V.YRI.VRLSRKRNEDEDSPNKLYTLVTYV.VTTFKNLQTVNVDEN
RetrocopyVLYRIHVRLSRKRNEDEDSPNKLYTLVTYVTVTTFKNLQTVNVDEN

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 418 .21 RPM
bodymap2_adrenal 0 .12 RPM 617 .22 RPM
bodymap2_brain 0 .00 RPM 228 .14 RPM
bodymap2_breast 0 .02 RPM 375 .16 RPM
bodymap2_colon 0 .06 RPM 724 .46 RPM
bodymap2_heart 0 .04 RPM 197 .05 RPM
bodymap2_kidney 0 .08 RPM 276 .37 RPM
bodymap2_liver 0 .11 RPM 260 .86 RPM
bodymap2_lung 0 .09 RPM 734 .42 RPM
bodymap2_lymph_node 0 .49 RPM 777 .29 RPM
bodymap2_ovary 0 .19 RPM 734 .99 RPM
bodymap2_prostate 0 .48 RPM 913 .89 RPM
bodymap2_skeletal_muscle 0 .25 RPM 392 .71 RPM
bodymap2_testis 0 .08 RPM 430 .21 RPM
bodymap2_thyroid 0 .11 RPM 334 .07 RPM
bodymap2_white_blood_cells 0 .57 RPM 958 .25 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1345 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1345 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_39090172 libraries172 libraries955 libraries277 libraries253 libraries

The graphical summary, for retro_hsap_1345 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_1345 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1345 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1047
Parental genes homology:
Parental genes homology involve 7 parental genes, and 102 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000071082 45 retrocopies
retro_hsap_1026, retro_hsap_1056, retro_hsap_1075, retro_hsap_1102, retro_hsap_1118, retro_hsap_1150, retro_hsap_1217, retro_hsap_1269, retro_hsap_1345 , retro_hsap_1527, retro_hsap_1691, retro_hsap_1856, retro_hsap_1865, retro_hsap_1993, retro_hsap_1998, retro_hsap_2215, retro_hsap_2246, retro_hsap_2388, retro_hsap_2470, retro_hsap_2510, retro_hsap_2610, retro_hsap_2615, retro_hsap_2627, retro_hsap_2839, retro_hsap_2921, retro_hsap_2959, retro_hsap_3108, retro_hsap_3325, retro_hsap_3471, retro_hsap_3472, retro_hsap_3525, retro_hsap_3731, retro_hsap_3777, retro_hsap_3788, retro_hsap_3899, retro_hsap_3965, retro_hsap_4070, retro_hsap_4210, retro_hsap_461, retro_hsap_4693, retro_hsap_506, retro_hsap_548, retro_hsap_677, retro_hsap_794, retro_hsap_831,
Gorilla gorilla ENSGGOG0000000643224 retrocopies
retro_ggor_1047, retro_ggor_113, retro_ggor_1442, retro_ggor_169, retro_ggor_1811, retro_ggor_1839, retro_ggor_192, retro_ggor_1971, retro_ggor_21, retro_ggor_2132, retro_ggor_2383, retro_ggor_2541, retro_ggor_2547, retro_ggor_2625, retro_ggor_2820, retro_ggor_442, retro_ggor_583, retro_ggor_655, retro_ggor_834, retro_ggor_84, retro_ggor_849, retro_ggor_874, retro_ggor_88, retro_ggor_997,
Latimeria chalumnae ENSLACG000000136031 retrocopy
retro_lcha_94,
Macropus eugenii ENSMEUG000000009638 retrocopies
retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Myotis lucifugus ENSMLUG0000000250721 retrocopies
retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Macaca mulatta ENSMMUG000000098731 retrocopy
retro_mmul_340,
Nomascus leucogenys ENSNLEG000000144442 retrocopies
retro_nleu_47, retro_nleu_530,

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 = 0.8 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .30 RPM
CEU_NA11843 0 .74 RPM
CEU_NA11930 0 .75 RPM
CEU_NA12004 0 .38 RPM
CEU_NA12400 0 .46 RPM
CEU_NA12751 0 .34 RPM
CEU_NA12760 0 .76 RPM
CEU_NA12827 0 .66 RPM
CEU_NA12872 0 .49 RPM
CEU_NA12873 0 .54 RPM
FIN_HG00183 0 .44 RPM
FIN_HG00277 0 .41 RPM
FIN_HG00315 0 .44 RPM
FIN_HG00321 0 .39 RPM
FIN_HG00328 0 .21 RPM
FIN_HG00338 0 .47 RPM
FIN_HG00349 0 .51 RPM
FIN_HG00375 0 .54 RPM
FIN_HG00377 0 .25 RPM
FIN_HG00378 0 .34 RPM
GBR_HG00099 0 .35 RPM
GBR_HG00111 0 .43 RPM
GBR_HG00114 0 .39 RPM
GBR_HG00119 0 .29 RPM
GBR_HG00131 0 .32 RPM
GBR_HG00133 0 .41 RPM
GBR_HG00134 0 .41 RPM
GBR_HG00137 0 .47 RPM
GBR_HG00142 0 .36 RPM
GBR_HG00143 0 .29 RPM
TSI_NA20512 0 .28 RPM
TSI_NA20513 0 .22 RPM
TSI_NA20518 0 .80 RPM
TSI_NA20532 0 .48 RPM
TSI_NA20538 0 .46 RPM
TSI_NA20756 0 .79 RPM
TSI_NA20765 0 .25 RPM
TSI_NA20771 0 .34 RPM
TSI_NA20786 0 .26 RPM
TSI_NA20798 0 .22 RPM
YRI_NA18870 0 .61 RPM
YRI_NA18907 0 .21 RPM
YRI_NA18916 0 .23 RPM
YRI_NA19093 0 .16 RPM
YRI_NA19099 0 .32 RPM
YRI_NA19114 0 .24 RPM
YRI_NA19118 0 .23 RPM
YRI_NA19213 0 .19 RPM
YRI_NA19214 0 .25 RPM
YRI_NA19223 0 .16 RPM

Indel association:

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





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