RetrogeneDB ID:

retro_hsap_141

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:40428218..40429073(+)
Located in intron of:ENSG00000168389
Retrocopy
information
Ensembl ID:ENSG00000228477
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_141
ATGGCGGATGACACTGGTGCAGCGGGGGGGCCTGGAGGCCCTGGTGGCCCTGGGATGGGGAACTCTGGTGCCTTCCGCGG
AGGTTTCGGCAGTGGCATCCGGGGCCGGGGTCATGGCCGTGGACGGGGCCCGGGCCGAAGCTGCGGAGCTTGCTGAGGCA
AGGCCGAGGATAAGGAGTGGATGCCTGTCACCAAGCTGGGCCGCTTGGTGAAGGACATGAAGATCAAGTCCCTGCAGGAG
ATCTATCTCTTCTCTCTGCCCATTAAGGGATCTGAGATCATTGACTTTTTCCTGGGGGCCTCTCTCAAGGATGAGGTTTT
GAAGATTATGCCAGTGCAGAAGCAGACCCGTGCCGGCCAGCGCACCAGGTTCAAGGCGTTTGTTGCTATCGGAGACTACA
ATGGCCATGTCGGTCTGGGTGTTAAGTGCTCCAAGGAGGTGGCCACCGCCATCCGTGGGGCCATCATCCTGGCCAAGCTC
TCCATTGTCCCCGTGCGCAGAGGCTACTGGGGGAACAAGATCAGCAAGCCCCACACCGTCCCTTGCAAGGTGACAGGCCG
CTGCGGCTCTGTGCTGGTGCGTCTCATCCCTGCACCCAGGAGCACTGGCATCGTCTCCACACCTGTGCCCAAGAAGCTGC
TCATGATGGCTGGTATCGATGACTGCTACACCTCAGCCCGGGGCTGCACTGCCACCCTGGGCAGCTTTGCCAAGGGCACC
TTTGATGCCATCTCTAAGACCTACAGCTACCTGACCCCCGACCTCTGGAAGGAGACTGTATTCACCAAGTCTCCCGATCA
GGAATTCACTGACCACCTCATCAAGACCCACCAGGCTCCAGCTGTGGCTACAACA

ORF - retro_hsap_141 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.58 %
Parental protein coverage: 97.27 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEWMPVTKLGRLV
MADD.GAAGGPGGPGGPGMGN.G.FRGGFGSGIRGRG.GRGRG.GR..GA..GKAEDKEWMPVTKLGRLV
RetrocopyMADDTGAAGGPGGPGGPGMGNSGAFRGGFGSGIRGRGHGRGRGPGRSCGAC*GKAEDKEWMPVTKLGRLV
ParentalKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLG
KDMKIKSL.EIYLFSLPIK.SEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLG
RetrocopyKDMKIKSLQEIYLFSLPIKGSEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLG
ParentalVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVP
VKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKI.KPHTVPCKVTGRCGSVLVRLIPAPR.TGIVS.PVP
RetrocopyVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKISKPHTVPCKVTGRCGSVLVRLIPAPRSTGIVSTPVP
ParentalKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV
KKLLMMAGIDDCYTSARGCTATLG.FAK.TFDAISKTYSYLTPDLWKETVFTKSP.QEFTDHL.KTH...
RetrocopyKKLLMMAGIDDCYTSARGCTATLGSFAKGTFDAISKTYSYLTPDLWKETVFTKSPDQEFTDHLIKTHQAP
ParentalSVQRT
.V..T
RetrocopyAVATT

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 496 .47 RPM
bodymap2_adrenal 0 .14 RPM 505 .10 RPM
bodymap2_brain 0 .12 RPM 53 .79 RPM
bodymap2_breast 0 .00 RPM 261 .89 RPM
bodymap2_colon 0 .06 RPM 444 .16 RPM
bodymap2_heart 0 .00 RPM 116 .21 RPM
bodymap2_kidney 0 .43 RPM 179 .65 RPM
bodymap2_liver 0 .76 RPM 249 .89 RPM
bodymap2_lung 1 .23 RPM 464 .79 RPM
bodymap2_lymph_node 0 .51 RPM 651 .42 RPM
bodymap2_ovary 0 .04 RPM 445 .62 RPM
bodymap2_prostate 0 .83 RPM 603 .00 RPM
bodymap2_skeletal_muscle 0 .04 RPM 731 .68 RPM
bodymap2_testis 0 .13 RPM 238 .89 RPM
bodymap2_thyroid 0 .21 RPM 257 .52 RPM
bodymap2_white_blood_cells 0 .02 RPM 782 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_141 was not detected