RetrogeneDB ID:

retro_hsap_4897

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:122250823..122251609(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000224236
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRRF
Ensembl ID:ENSG00000148187
Aliases:MRRF, MRFF, MTRRF, RRF
Description:mitochondrial ribosome recycling factor [Source:HGNC Symbol;Acc:7234]


Retrocopy-Parental alignment summary:






>retro_hsap_4897
ATGGCCTTGGGATTAAAGTGCTCCCGCATGGTCCACCCTGCCTTTCGCAATTATCTTGCAGCCTCTATCAGACCCGTTTC
AGAAGTTACACTGAAGAAAGTGTATGAAAGACAACATGGCCATAGGCAATACGTGGCCTATTCAGCTGTACCAGTCCACC
ATTTTGCTACCAAGAAAGCCAAAGCCAAAGGGAAAGGAAAGTCCCAAACCAGAGTGAATATTAGTGCTGCCTTTGTTGAG
GATATAATCAACTTGGAAGAGGTGAATGAAGAAATGAAGTCTGTGATAGAAGCACGCAAGGATAATTTCAATAAGACTCT
CAATATAGGGACCTCACCAGGATCCCTTGACAAGATTGCTGTGGTAACCGCTGATGGAAAACTTGCTTTAAACCAGATTA
GGCAGATCTCCGTGAAGTTGCCACAGCTGATTTTGGTGAATATGGCCAGCTTCCCAGAGTTCACAGTTGCAGCTATCAAG
GCTATAAGAGAAAGTGGAATGAATCTGAACCCAGAAGTGGAAGGGACACTAATTCGGGTACCCATTCCCCAAGTAATCAG
AGAGCACAGAGAAATGCTGGTGAAACTGGCCAAACAGAACACCAACAAGGCCACATACTCTTTACGGAAGGTTTGTACCA
ACGCAATGAACAAGCTGAAGAAATCCAAGGATACAGTCTCGGAGGGCACCATTAGGCTAACAGAGAAACAGATCAGCCAA
ATGGCCGATGACACAGTGGCAGAACTGTACAGGCATCTGGCAGTGAAGACCAAAGAACTCCTTGGA

ORF - retro_hsap_4897 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.84 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALGLKCFRMVHPTFRNYLAASIRPVSEVTLKTVHERQHGHRQYMAYSAVPVRHFATKKAKAKGKGQSQT
MALGLKC.RMVHP.FRNYLAASIRPVSEVTLK.V.ERQHGHRQY.AYSAVPV.HFATKKAKAKGKG.SQT
RetrocopyMALGLKCSRMVHPAFRNYLAASIRPVSEVTLKKVYERQHGHRQYVAYSAVPVHHFATKKAKAKGKGKSQT
ParentalRVNINAALVEDIINLEEVNEEMKSVIEALKDNFNKTLNIRTSPGSLDKIAVVTADGKLALNQISQISMKS
RVNI.AA.VEDIINLEEVNEEMKSVIEA.KDNFNKTLNI.TSPGSLDKIAVVTADGKLALNQI.QIS.K.
RetrocopyRVNISAAFVEDIINLEEVNEEMKSVIEARKDNFNKTLNIGTSPGSLDKIAVVTADGKLALNQIRQISVKL
ParentalPQLILVNMASFPECTAAAIKAIRESGMNLNPEVEGTLIRVPIPQVTREHREMLVKLAKQNTNKAKDSLRK
PQLILVNMASFPE.T.AAIKAIRESGMNLNPEVEGTLIRVPIPQV.REHREMLVKLAKQNTNKA..SLRK
RetrocopyPQLILVNMASFPEFTVAAIKAIRESGMNLNPEVEGTLIRVPIPQVIREHREMLVKLAKQNTNKATYSLRK
ParentalVRTNSMNKLKKSKDTVSEDTIRLIEKQISQMADDTVAELDRHLAVKTKELLG
V.TN.MNKLKKSKDTVSE.TIRL.EKQISQMADDTVAEL.RHLAVKTKELLG
RetrocopyVCTNAMNKLKKSKDTVSEGTIRLTEKQISQMADDTVAELYRHLAVKTKELLG

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 18 .03 RPM
bodymap2_adrenal 0 .00 RPM 25 .10 RPM
bodymap2_brain 0 .00 RPM 7 .92 RPM
bodymap2_breast 0 .00 RPM 12 .14 RPM
bodymap2_colon 0 .00 RPM 11 .95 RPM
bodymap2_heart 0 .00 RPM 19 .05 RPM
bodymap2_kidney 0 .00 RPM 29 .78 RPM
bodymap2_liver 0 .00 RPM 15 .95 RPM
bodymap2_lung 0 .00 RPM 14 .10 RPM
bodymap2_lymph_node 0 .00 RPM 15 .79 RPM
bodymap2_ovary 0 .00 RPM 14 .84 RPM
bodymap2_prostate 0 .00 RPM 20 .84 RPM
bodymap2_skeletal_muscle 0 .00 RPM 18 .93 RPM
bodymap2_testis 0 .19 RPM 19 .74 RPM
bodymap2_thyroid 0 .00 RPM 21 .71 RPM
bodymap2_white_blood_cells 0 .00 RPM 12 .68 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4897 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4897 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_19688069 libraries10 libraries450 libraries814 libraries486 libraries

The graphical summary, for retro_hsap_4897 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_4897 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4897 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3265
Gorilla gorilla retro_ggor_98
Pongo abelii retro_pabe_80
Parental genes homology:
Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000073511 retrocopy
retro_cpor_877,
Homo sapiens ENSG00000148187 1 retrocopy
retro_hsap_4897 ,
Gorilla gorilla ENSGGOG000000234991 retrocopy
retro_ggor_98,
Mus musculus ENSMUSG000000268871 retrocopy
retro_mmus_340,
Nomascus leucogenys ENSNLEG000000171771 retrocopy
retro_nleu_1263,
Pongo abelii ENSPPYG000000195701 retrocopy
retro_pabe_80,
Pan troglodytes ENSPTRG000000213241 retrocopy
retro_ptro_3265,
Rattus norvegicus ENSRNOG000000259972 retrocopies
retro_rnor_1477, retro_rnor_2654,
Sarcophilus harrisii ENSSHAG000000124692 retrocopies
retro_shar_610, retro_shar_704,
Tupaia belangeri ENSTBEG000000165691 retrocopy
retro_tbel_4411,

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 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 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 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 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 .03 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 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017