RetrogeneDB ID:

retro_hsap_2772

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:37058013..37058478(-)
Located in intron of:ENSG00000076242
Retrocopy
information
Ensembl ID:ENSG00000224858
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL29
Ensembl ID:ENSG00000162244
Aliases:RPL29, HIP, HUMRPL29, L29, RPL29P10, RPL29_3_370
Description:ribosomal protein L29 [Source:HGNC Symbol;Acc:10331]


Retrocopy-Parental alignment summary:






>retro_hsap_2772
ATGGCGAAGTCCAAGAACCACACCACACACAACCAGTCCCGAAAATGGCACAGAAATGGTATCAAGAAACCCCGATCACA
AAGATACGAATCTCTTAAGGGGGTGGACCCCAAGTTCCTGAGGAACATGCACTTTGCCAAGAAGCACAACAAGAAGGGCC
TAAAGAAGATGCAGGCCAACAATGCCAAGGCCATGAGTGCACGTGCCGAGGCTATCAAGGCCCTCGTAAAGCCCAAGGAG
GTTAAGCCCAAGATCCCAAAGGGTGTCAGCCGCAAGCTCGATCGACTTGCCTACATTGCCCATCCCAAGCTTGGGAAGCG
TGCTCGTGCCCGTATTGCCAAGGGGCTCAGGCTGTGCCGGCCAAAGGCCAAGGCCAAGGATCAAACCAAGGCCCAGGCTG
CAGCTCCACCTTCAGTTCCAGCTCAGGCTCCCAAAGGTGCCCAGGCCCCTACAAAGGCTTCAGAG

ORF - retro_hsap_2772 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.97 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQANNAKAMSARAE
MAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNM.FAKKHNKKGLKKMQANNAKAMSARAE
RetrocopyMAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMHFAKKHNKKGLKKMQANNAKAMSARAE
ParentalAIKALVKPKEVKPKIPKGVSRKLDRLAYIAHPKLGKRARARIAKGLRLCRPKAKAKAKAKDQTKAQAAAP
AIKALVKPKEVKPKIPKGVSRKLDRLAYIAHPKLGKRARARIAKGLRLCRPKAKAK....DQTKAQAAAP
RetrocopyAIKALVKPKEVKPKIPKGVSRKLDRLAYIAHPKLGKRARARIAKGLRLCRPKAKAK----DQTKAQAAAP
ParentalASVPAQAPKRTQAPTKASE
.SVPAQAPK..QAPTKASE
RetrocopyPSVPAQAPKGAQAPTKASE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .42 RPM 345 .40 RPM
bodymap2_adrenal 0 .45 RPM 368 .49 RPM
bodymap2_brain 0 .23 RPM 44 .84 RPM
bodymap2_breast 0 .16 RPM 226 .07 RPM
bodymap2_colon 0 .04 RPM 351 .62 RPM
bodymap2_heart 0 .09 RPM 82 .58 RPM
bodymap2_kidney 0 .00 RPM 143 .27 RPM
bodymap2_liver 0 .00 RPM 120 .41 RPM
bodymap2_lung 0 .30 RPM 323 .61 RPM
bodymap2_lymph_node 0 .57 RPM 374 .43 RPM
bodymap2_ovary 0 .50 RPM 388 .74 RPM
bodymap2_prostate 0 .17 RPM 379 .29 RPM
bodymap2_skeletal_muscle 0 .22 RPM 419 .30 RPM
bodymap2_testis 0 .06 RPM 194 .98 RPM
bodymap2_thyroid 0 .32 RPM 207 .95 RPM
bodymap2_white_blood_cells 0 .00 RPM 354 .52 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_2772 was not detected
No EST(s) were mapped for retro_hsap_2772 retrocopy.


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_134414504 libraries865 libraries450 libraries9 libraries1 library

The graphical summary, for retro_hsap_2772 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)

retro_hsap_2772 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2772 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1929

Parental genes homology:
Parental genes homology involve 18 parental genes, and 186 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091636 retrocopies
Callithrix jacchus ENSCJAG000000059519 retrocopies
Felis catus ENSFCAG000000017629 retrocopies
Homo sapiens ENSG00000162244 23 retrocopies
Gorilla gorilla ENSGGOG0000002469116 retrocopies
Microcebus murinus ENSMICG000000027059 retrocopies
Myotis lucifugus ENSMLUG0000001508814 retrocopies
Macaca mulatta ENSMMUG000000192482 retrocopies
Monodelphis domestica ENSMODG0000002875017 retrocopies
Mustela putorius furoENSMPUG000000117346 retrocopies
Mus musculus ENSMUSG000000487583 retrocopies
Otolemur garnettii ENSOGAG000000137662 retrocopies
Ochotona princeps ENSOPRG0000000882110 retrocopies
Pongo abelii ENSPPYG0000001381821 retrocopies
Rattus norvegicus ENSRNOG0000001113815 retrocopies
Sorex araneus ENSSARG000000135728 retrocopies
Sarcophilus harrisii ENSSHAG000000068542 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000002048814 retrocopies

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 = 0.69 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .26 RPM
CEU_NA11843 0 .28 RPM
CEU_NA11930 0 .33 RPM
CEU_NA12004 0 .27 RPM
CEU_NA12400 0 .28 RPM
CEU_NA12751 0 .36 RPM
CEU_NA12760 0 .27 RPM
CEU_NA12827 0 .38 RPM
CEU_NA12872 0 .41 RPM
CEU_NA12873 0 .45 RPM
FIN_HG00183 0 .69 RPM
FIN_HG00277 0 .26 RPM
FIN_HG00315 0 .39 RPM
FIN_HG00321 0 .39 RPM
FIN_HG00328 0 .28 RPM
FIN_HG00338 0 .21 RPM
FIN_HG00349 0 .28 RPM
FIN_HG00375 0 .34 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .34 RPM
GBR_HG00099 0 .17 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .22 RPM
GBR_HG00131 0 .29 RPM
GBR_HG00133 0 .19 RPM
GBR_HG00134 0 .26 RPM
GBR_HG00137 0 .36 RPM
GBR_HG00142 0 .36 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .31 RPM
TSI_NA20513 0 .24 RPM
TSI_NA20518 0 .36 RPM
TSI_NA20532 0 .24 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .20 RPM
TSI_NA20765 0 .23 RPM
TSI_NA20771 0 .31 RPM
TSI_NA20786 0 .18 RPM
TSI_NA20798 0 .37 RPM
YRI_NA18870 0 .51 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .15 RPM
YRI_NA19093 0 .13 RPM
YRI_NA19099 0 .19 RPM
YRI_NA19114 0 .29 RPM
YRI_NA19118 0 .25 RPM
YRI_NA19213 0 .33 RPM
YRI_NA19214 0 .15 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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