RetrogeneDB ID:

retro_hsap_397

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:63106790..63107364(-)
Located in intron of:ENSG00000116641
Retrocopy
information
Ensembl ID:ENSG00000213703
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL13A
Ensembl ID:ENSG00000142541
Aliases:RPL13A, L13A, TSTA1
Description:ribosomal protein L13a [Source:HGNC Symbol;Acc:10304]


Retrocopy-Parental alignment summary:






>retro_hsap_397
GGCTGAGGCCATCTCCGGGTTGCCCAGCGGCCATTGTGGCCAAGCAGGTACTGCTGGGCTGGAAGGTGGTGATCATGTGT
TGCGAGGGCATCCACATTTCTGGCAATTTCTACAGAAACAAGTTAAAGTACCTGGCCTTCCTCTGCAAGTAGATGAACAC
CAATCCTTTCTGAGGACCCTACCATTTCCAAGCCCCCAGCCACCTCTTTTGGTGGACCATGTGAAGCATGCTGCCCCACA
AGACCAAGTGAGGCCAGGCTGCTTTGGACCACCTCAAGATGTTTGATGGGATCCCACTCCCCTATGACAAAAAGTGGACT
GTGGTTCCTGCTGCCCTCAAGGTTGTGTGCCTGAAGCCTGTGAGAAAGTTTGCCTACCTGGGGCTCCTGGCTCATGGTGT
TGGCTGGAAGTACCAGGCAGTGACAGCCACCATGGAGAAGAAGAGAAAGAAGAAAGCTAAGATCCACTACTGGAAGAAAA
GACAGCTCATGAGTCTATAGAAACAGGCCAAAAGAACATGGAGAAGAAAACTGACAAATACATAGAGGTCCTCAAGAGCC
ATGGACTCCTGGTC

ORF - retro_hsap_397 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.92 %
Parental protein coverage: 95.07 %
Number of stop codons detected: 6
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGRGHLL-GRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRGPYHFRAPSRI
G.GHL..G..AAIVAKQVLLG.KVV...CEGI.ISGNFYRNKLKYLAFL.K.MNTNP..GPYHF.APS..
RetrocopyG*GHLR<GCPAAIVAKQVLLGWKVVIMCCEGIHISGNFYRNKLKYLAFLCK*MNTNPF*GPYHFQAPSHL
ParentalFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEVGWKY
FW.T...MLPHKTK.GQAALD.LK.FDGIP.PYD.KK..VVPAALKVV.LKP.RKFAYLG.LAH.VGWKY
RetrocopyFWWTM*SMLPHKTK*GQAALDHLKMFDGIPLPYD-KKWTVVPAALKVVCLKPVRKFAYLGLLAHGVGWKY
ParentalQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQA-EKNVEKKIDKYTEVLKTHGLLV
QAVTAT.E.KRK.KAKIHY.KK.QLM.L.KQA..KN.EKK.DKY.EVLK.HGLLV
RetrocopyQAVTATMEKKRKKKAKIHYWKKRQLMSL*KQA<QKNMEKKTDKYIEVLKSHGLLV

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 967 .42 RPM
bodymap2_adrenal 0 .00 RPM 1518 .40 RPM
bodymap2_brain 0 .02 RPM 156 .35 RPM
bodymap2_breast 0 .00 RPM 689 .11 RPM
bodymap2_colon 0 .00 RPM 1303 .66 RPM
bodymap2_heart 0 .02 RPM 269 .24 RPM
bodymap2_kidney 0 .00 RPM 446 .76 RPM
bodymap2_liver 0 .04 RPM 328 .33 RPM
bodymap2_lung 0 .00 RPM 1095 .62 RPM
bodymap2_lymph_node 0 .00 RPM 1494 .82 RPM
bodymap2_ovary 0 .02 RPM 1466 .56 RPM
bodymap2_prostate 0 .00 RPM 1422 .20 RPM
bodymap2_skeletal_muscle 0 .00 RPM 598 .29 RPM
bodymap2_testis 0 .00 RPM 649 .24 RPM
bodymap2_thyroid 0 .00 RPM 674 .57 RPM
bodymap2_white_blood_cells 0 .00 RPM 1717 .29 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_397 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_397 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_397 retrocopy 5' end.

Lab - click to see more details

retro_hsap_397 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_397 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Callithrix jacchus retro_cjac_3009
Parental genes homology:
Parental genes homology involve 10 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000052963 retrocopies
retro_btau_1251, retro_btau_719, retro_btau_789,
Canis familiaris ENSCAFG000000298923 retrocopies
retro_cfam_1772, retro_cfam_924, retro_cfam_976,
Callithrix jacchus ENSCJAG0000000007216 retrocopies
retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Echinops telfairi ENSETEG000000170762 retrocopies
retro_etel_46, retro_etel_853,
Homo sapiens ENSG00000142541 22 retrocopies
retro_hsap_1072, retro_hsap_1100, retro_hsap_1111, retro_hsap_1268, retro_hsap_1410, retro_hsap_2200, retro_hsap_2500, retro_hsap_293, retro_hsap_298, retro_hsap_3173, retro_hsap_3350, retro_hsap_3444, retro_hsap_3652, retro_hsap_3752, retro_hsap_3772, retro_hsap_397 , retro_hsap_436, retro_hsap_615, retro_hsap_671, retro_hsap_730, retro_hsap_753, retro_hsap_967,
Loxodonta africana ENSLAFG000000162133 retrocopies
retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Mus musculus ENSMUSG000000741293 retrocopies
retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Pteropus vampyrus ENSPVAG000000109583 retrocopies
retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus ENSRNOG0000002061810 retrocopies
retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa ENSSSCG000000031664 retrocopies
retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,

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 = 0.08 RPM Legend:


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