RetrogeneDB ID:

retro_hsap_1444

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:76304926..76305544(-)
Located in intron of:ENSG00000119685
Retrocopy
information
Ensembl ID:ENSG00000242488
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS2
Ensembl ID:ENSG00000140988
Aliases:RPS2, LLREP3, S2
Description:ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]


Retrocopy-Parental alignment summary:






>retro_hsap_1444
GGTCTAGACCGCAGGTGTGCTCAGGGCCCACACCACAGAGCTCACAGAAGCAAGACCAAGTACAAGGAGTGTGTCACCAT
CCGCATGCTGGGCTGCCTGGACAAGAACATGAAAATCAAGTCCCTGGAGCAGATCTCTCTCTTCTCCCTGCCCATCAAGG
AATCTGAGATCATCGACATTTCTGGGGACACCCTCTCACAGGTGAGGTTTTGAAGACTATACTTGTGGCAAAAGCAGACC
CACACTGGCCAGTGGACCAGGTTCAAGGCATTTGTTACCATAAGGGACTACAATGGCTACATCAGTCTGGATAATTGCTC
CAAGGAGGCGGACAGTAGCATCTGTGGGGTTATCACCCTGCTCTCCATCATCCCCATGCAGCAAGGATCCAATGGAACAA
GATCAGCAAGCTCCACACTCTGCACTGCAAGTGACTGGCTGCTGCGGCTCTGTGCTGATGTGCCTCACCCTCGCCCCCAA
AGGCACTGTCAACATCTTAGGTCCTGCACTCAAAAAGCTGCTGCTTATACCTGGTACTCATGACTGCTACACCTTAGCCA
GGGGTTGCACCACCCTCTGAGCAACTGTGCCAAGACTACCTTTGATGCCACCTCCAAG

ORF - retro_hsap_1444 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.35 %
Parental protein coverage: 71.67 %
Number of stop codons detected: 0
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalGRGRGRGRGRGRGARGGKAEDKEWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDF-FLGASLKDE
G..R....G....A...K...KE......LG.L.K.MKIKSLE.I.LFSLPIKESEIID..F.G..L..E
RetrocopyGLDRRCAQGPHHRAHRSKTKYKECVTIRMLGCLDKNMKIKSLEQISLFSLPIKESEIIDI<FWGHPLTGE
ParentalVLKIMPV-QKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWG-NK
VLK...V.QKQT..GQ.TRFKAFV.I.DYNG...L...CSKE....I.G.I.L..LSI.P...G..G.NK
RetrocopyVLKTILV>QKQTHTGQWTRFKAFVTIRDYNGYISLD-NCSKEADSSICGVITL--LSIIPMQQGSNG<NK
ParentalIGKPHTVPCK-VTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTA-TLGNFAKATF
I.K.HT..CK.VTG.CGSVL..L..AP.GT.....P..KKLL...G..DCYT.ARGCT...L.N.AK.TF
RetrocopyISKLHTLHCK<VTGCCGSVLMCLTLAPKGTVNILGPALKKLLLIPGTHDCYTLARGCTT<PLSNCAKTTF
ParentalDAISK
DA.SK
RetrocopyDATSK

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 .00 RPM 496 .47 RPM
bodymap2_adrenal 0 .12 RPM 505 .10 RPM
bodymap2_brain 0 .00 RPM 53 .79 RPM
bodymap2_breast 0 .00 RPM 261 .89 RPM
bodymap2_colon 0 .00 RPM 444 .16 RPM
bodymap2_heart 0 .17 RPM 116 .21 RPM
bodymap2_kidney 0 .00 RPM 179 .65 RPM
bodymap2_liver 0 .13 RPM 249 .89 RPM
bodymap2_lung 0 .00 RPM 464 .79 RPM
bodymap2_lymph_node 0 .00 RPM 651 .42 RPM
bodymap2_ovary 0 .00 RPM 445 .62 RPM
bodymap2_prostate 0 .00 RPM 603 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 731 .68 RPM
bodymap2_testis 0 .00 RPM 238 .89 RPM
bodymap2_thyroid 0 .00 RPM 257 .52 RPM
bodymap2_white_blood_cells 0 .00 RPM 782 .33 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_1444 was not detected
No EST(s) were mapped for retro_hsap_1444 retrocopy.
No TSS is located nearby retro_hsap_1444 retrocopy 5' end.
retro_hsap_1444 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1444 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 6 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000025491 retrocopy
Felis catus ENSFCAG000000291916 retrocopies
Homo sapiens ENSG00000140988 47 retrocopies
Monodelphis domestica ENSMODG000000160771 retrocopy
Otolemur garnettii ENSOGAG0000001009819 retrocopies
Sarcophilus harrisii ENSSHAG000000152135 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 = 0.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 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 .00 RPM
YRI_NA19214 0 .05 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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