RetrogeneDB ID:

retro_hsap_2500

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:21:26734134..26734742(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213885
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_2500
ATGGCGGAGGTGCAGGTCCTGGTGCTCGATGGTCGAGGCCATCTCCTGGTCCGCCTGGCGGCCATCGTGGCTAAACAGGT
ACTGCTGGGCCGGAAAGTGGTGGTCGTACGCTGCGAAGGCATCAACATTTCTGGCAATTTCTACAGAAACAAGTTGAAGT
ACCTGGGTTTCCTCCGCAAGCGGATGAACACCCACCTTTCCCGAGGTCCCTACCACTTCCGGGCCCCCCAGCCGCATCTT
CTGGCGGACCGTGCGAGGTATGCCGCCCCACAAGACCAAGCGAGGCCAGGCTTCTCTGGACCGCCTCAAGGTGTTTGACC
GCATCCCACCGCCCTACGACAAGAAAAAGCGGATGGTGTTCCTGCTCCCTCAAGGTTGTGCGTCTGAAGCCTACAAGAAA
GTTTGCCTATCTGGGGCGCCTGGCTCACGAGGTTGGCTGGAAGTACCAGGCAGTGACAGCCACCCTGGAGGAGAAGAGGA
AAGAGAAAGCCAAGATCCACTACCGGAAGAAGAAACAGCTCATGAGGCTACGGAAACAGGCCGAGAAGAACATGGAGAAG
AAAATTGACAAATACACAGAGGTCCTCAAGACCCACAGACTCCTGGTC

ORF - retro_hsap_2500 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.69 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAEVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRGP
MAEVQVLVLDGRGHLL.RLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYL.FLRKRMNT..SRGP
RetrocopyMAEVQVLVLDGRGHLLVRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLGFLRKRMNTHLSRGP
ParentalYHFRAP-SRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMV-VPA-ALKVVRLKPTRKFAY
YHFRAP.SRIFWRTVRGM.PHKTKRGQA.LDRLKVFD.IPPPYDKKKRMV.VPA..LKVVRLKPTRKFAY
RetrocopyYHFRAP>SRIFWRTVRGMPPHKTKRGQASLDRLKVFDRIPPPYDKKKRMV<VPA<SLKVVRLKPTRKFAY
ParentalLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLLV
LGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKN.EKKIDKYTEVLKTH.LLV
RetrocopyLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNMEKKIDKYTEVLKTHRLLV

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 .18 RPM 967 .42 RPM
bodymap2_adrenal 0 .23 RPM 1518 .40 RPM
bodymap2_brain 0 .07 RPM 156 .35 RPM
bodymap2_breast 0 .10 RPM 689 .11 RPM
bodymap2_colon 0 .04 RPM 1303 .66 RPM
bodymap2_heart 0 .04 RPM 269 .24 RPM
bodymap2_kidney 0 .12 RPM 446 .76 RPM
bodymap2_liver 0 .06 RPM 328 .33 RPM
bodymap2_lung 0 .18 RPM 1095 .62 RPM
bodymap2_lymph_node 0 .20 RPM 1494 .82 RPM
bodymap2_ovary 0 .13 RPM 1466 .56 RPM
bodymap2_prostate 0 .28 RPM 1422 .20 RPM
bodymap2_skeletal_muscle 0 .20 RPM 598 .29 RPM
bodymap2_testis 0 .49 RPM 649 .24 RPM
bodymap2_thyroid 0 .02 RPM 674 .57 RPM
bodymap2_white_blood_cells 0 .22 RPM 1717 .29 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2500 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2500 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_104155991 libraries297 libraries407 libraries100 libraries34 libraries

The graphical summary, for retro_hsap_2500 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_2500 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2500 has 0 orthologous retrocopies within eutheria group .

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 = 2.27 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .03 RPM
CEU_NA11843 2 .27 RPM
CEU_NA11930 1 .40 RPM
CEU_NA12004 2 .09 RPM
CEU_NA12400 2 .10 RPM
CEU_NA12751 1 .24 RPM
CEU_NA12760 0 .72 RPM
CEU_NA12827 0 .85 RPM
CEU_NA12872 1 .80 RPM
CEU_NA12873 1 .34 RPM
FIN_HG00183 1 .24 RPM
FIN_HG00277 2 .07 RPM
FIN_HG00315 1 .66 RPM
FIN_HG00321 1 .48 RPM
FIN_HG00328 2 .08 RPM
FIN_HG00338 2 .07 RPM
FIN_HG00349 1 .65 RPM
FIN_HG00375 1 .42 RPM
FIN_HG00377 1 .41 RPM
FIN_HG00378 1 .08 RPM
GBR_HG00099 1 .37 RPM
GBR_HG00111 1 .50 RPM
GBR_HG00114 1 .55 RPM
GBR_HG00119 1 .60 RPM
GBR_HG00131 1 .72 RPM
GBR_HG00133 1 .45 RPM
GBR_HG00134 1 .51 RPM
GBR_HG00137 1 .29 RPM
GBR_HG00142 1 .33 RPM
GBR_HG00143 1 .31 RPM
TSI_NA20512 1 .33 RPM
TSI_NA20513 2 .13 RPM
TSI_NA20518 2 .08 RPM
TSI_NA20532 1 .02 RPM
TSI_NA20538 0 .88 RPM
TSI_NA20756 1 .34 RPM
TSI_NA20765 1 .12 RPM
TSI_NA20771 2 .18 RPM
TSI_NA20786 1 .86 RPM
TSI_NA20798 1 .25 RPM
YRI_NA18870 1 .05 RPM
YRI_NA18907 1 .56 RPM
YRI_NA18916 1 .81 RPM
YRI_NA19093 0 .81 RPM
YRI_NA19099 1 .22 RPM
YRI_NA19114 1 .34 RPM
YRI_NA19118 1 .08 RPM
YRI_NA19213 1 .75 RPM
YRI_NA19214 0 .96 RPM
YRI_NA19223 1 .63 RPM

Indel association:

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





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