RetrogeneDB ID:

retro_hsap_2957

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:88331880..88332537(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000249262
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPL19
Ensembl ID:ENSG00000115364
Aliases:None
Description:mitochondrial ribosomal protein L19 [Source:HGNC Symbol;Acc:14052]


Retrocopy-Parental alignment summary:






>retro_hsap_2957
CAGTTCTTGAGTCCCTAATTCATTCCTCCAAGGGGAAGAATAAATCCTCTGAAGTTTCAAATAGGAAGAAAAGTTATGTT
AGAGAGGAGAAAAGTACTCCACATTCCAGAGTTCTATGTTGGAAGTATTCTTTGTGTTACTACAGCTGACTCATATGCCA
GTGAAAAAATCAGCCAGTTTCTGGGGATTTGCATCTAGAGATCAGGAAAAGGACTTGGGGCTACTTTTATCCTTAGGAAT
GTTATTGAAGGACAAGGTGTTAAAATTTGCTTTGAACTTTATAATCCTCGAATCCGGGAGACTCAAGTGGTCAAATTAGA
GAAATGGGTGGATGATAGCTTGCTGTGGTTACGAGATGCTTTTCCTGAATATAGCACTGTTGATGTGAATATGAAGCCAG
TAGCACAAGAGCCTAGCCAAGAAGTTCCTGTTAATAAGCTGAAAATGAAAATGAAGCCTCAGCCCTGGTCCAAATGCTGG
GACTGTCCAAATTTTAATATTTAAGGAATAATATTTGATCCTTGTTTCACTGAAGAACAAATGAAAGCAGCTTAGAAGTA
GAGACAGCTGTGGCTTGAATTTGATACGATGAGGGAATATGATGCTTTAAAAATTGAAGCTGCAATATGGGATGAAAATG
AAGCATCCAGAAAGTCC

ORF - retro_hsap_2957 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.54 %
Parental protein coverage: 75. %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRFLSPEFIPRRGRTDPLKFQIERKDMLERRKVLHIPEFYVGSILRVTTADPYASGKISQFLGICIQRSGR
.FLSP.FIP.RGR..PLKFQI.RK.MLERRKVLHIPEFYVGSIL.VTTAD.YAS.KISQFLGICI.RSG.
RetrocopyQFLSP*FIPPRGRINPLKFQIGRKVMLERRKVLHIPEFYVGSILCVTTADSYASEKISQFLGICI*RSGK
ParentalGLGATFILRNVIEGQGVEICFELYNPRVQEIQVVKLEKRLDDSLLYLRDALPEYSTFDVNMKPVVQEPNQ
GLGATFILRNVIEGQGV.ICFELYNPR..E.QVVKLEK..DDSLL.LRDA.PEYST.DVNMKPV.QEP.Q
RetrocopyGLGATFILRNVIEGQGVKICFELYNPRIRETQVVKLEKWVDDSLLWLRDAFPEYSTVDVNMKPVAQEPSQ
ParentalKVPVNELKVKMKPKPWSKRWERPNFNIKGIRFDLCLTEQQMKEAQKWNQPWLEFDMMREYDTSKIEAAIW
.VPVN.LK.KMKP.PWSK.W..PNFNI.GI.FD.C.TE.QMK.A.K..Q.WLEFD.MREYD..KIEAAIW
RetrocopyEVPVNKLKMKMKPQPWSKCWDCPNFNI*GIIFDPCFTEEQMKAA*K*RQLWLEFDTMREYDALKIEAAIW
ParentalKEIEASKRS
.E.EAS..S
RetrocopyDENEASRKS

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 21 .91 RPM
bodymap2_adrenal 0 .00 RPM 29 .09 RPM
bodymap2_brain 0 .00 RPM 29 .96 RPM
bodymap2_breast 0 .00 RPM 40 .53 RPM
bodymap2_colon 0 .00 RPM 29 .87 RPM
bodymap2_heart 0 .00 RPM 33 .88 RPM
bodymap2_kidney 0 .00 RPM 48 .62 RPM
bodymap2_liver 0 .00 RPM 53 .27 RPM
bodymap2_lung 0 .00 RPM 16 .26 RPM
bodymap2_lymph_node 0 .00 RPM 23 .06 RPM
bodymap2_ovary 0 .00 RPM 30 .71 RPM
bodymap2_prostate 0 .00 RPM 24 .16 RPM
bodymap2_skeletal_muscle 0 .00 RPM 33 .65 RPM
bodymap2_testis 0 .00 RPM 31 .24 RPM
bodymap2_thyroid 0 .00 RPM 36 .25 RPM
bodymap2_white_blood_cells 0 .00 RPM 35 .48 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2957 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2957 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2957 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2957 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2957 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2002
Gorilla gorilla retro_ggor_2048
Pongo abelii retro_pabe_2453
Parental genes homology:
Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG000000022661 retrocopy
retro_eeur_485,
Homo sapiens ENSG00000115364 1 retrocopy
retro_hsap_2957 ,
Gorilla gorilla ENSGGOG000000278961 retrocopy
retro_ggor_2048,
Loxodonta africana ENSLAFG000000001461 retrocopy
retro_lafr_472,
Myotis lucifugus ENSMLUG000000127741 retrocopy
retro_mluc_1308,
Pongo abelii ENSPPYG000000122551 retrocopy
retro_pabe_2453,
Pan troglodytes ENSPTRG000000121081 retrocopy
retro_ptro_2002,
Ictidomys tridecemlineatus ENSSTOG000000028731 retrocopy
retro_itri_549,
Tupaia belangeri ENSTBEG000000164701 retrocopy
retro_tbel_326,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 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 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 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 .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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