RetrogeneDB ID:

retro_hsap_2283

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:80389576..80390335(-)
Located in intron of:ENSG00000066032
Retrocopy
information
Ensembl ID:ENSG00000223427
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBM7
Ensembl ID:ENSG00000076053
Aliases:None
Description:RNA binding motif protein 7 [Source:HGNC Symbol;Acc:9904]


Retrocopy-Parental alignment summary:






>retro_hsap_2283
TTTGTGGGCAACCTTGAAATGAAAGTGACCGAGGAGCTCCTTTTCGAGGTTTTCCACCAGGCTGGGCCAGTAATAAAGGT
GAAATTCCAAAAGATAAGGATGGTAAACCAAAGCAGTTTGCGTTTGTGAATTTCAAACATGAAGTATCTGTTCCTTATGC
AATGAATCTACTTAATGGAATCAAACTTTATGGAAGGCCTATCAAAATTCAATTTAGATCAGGAAGTAGTCATGCCTCGC
AAGATGTCAGTTTGCCATATCCCCAATATCATGTTGGAAATTCAAGCCCTACCTCCACAACTCCTAGCAGGTACGAAAGG
ACTAGGGATAACATGACTTCATCAGCACAGATAATTCAGAGATCTTTCTCTTCTCCAGAAAATTTTCAGAGACAAGCAGT
GATGAACAGTGCTTTGAGACAAATGTCATATGGTGGAAAATTTGCTTCTTCACCTCTGGATCAATCAGGATTTTCACCAT
CAGTTCAATCACACAGTCATAGTTTTAATCAGTCTTCAAGCTCCCAGTGGCGCCAAGGTACACCATCATCACAGCGTAAA
GTCAGAATGAATTCTCATCCCTACCTAGCAGATAGACATTATAGCCGGGAACAGCGTTACACTGATCATGGGTCTGACCA
TCATTACAGAGGAAAGAGATGATTTCTTCTATGAAGATAGGAATCATGATGGCTGGAGCCATGACTATGATAACAGAAGA
GACAGTAGCAGAGATGGAAAATGGCGCTCATCTCGACAC

ORF - retro_hsap_2283 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.53 %
Parental protein coverage: 95.49 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalFVGNLETKVTEELLFELFHQAGPVIKVK-IPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPIK
FVGNLE.KVTEELLFE.FHQAGPVIKVK.IPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPIK
RetrocopyFVGNLEMKVTEELLFEVFHQAGPVIKVK<IPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPIK
ParentalIQFRSGSSHAPQDVSLSYPQHHVGNSSPTSTSPSRYERTMDNMTSSAQIIQRSFSSPENFQRQAVMNSAL
IQFRSGSSHA.QDVSL.YPQ.HVGNSSPTST.PSRYERT.DNMTSSAQIIQRSFSSPENFQRQAVMNSAL
RetrocopyIQFRSGSSHASQDVSLPYPQYHVGNSSPTSTTPSRYERTRDNMTSSAQIIQRSFSSPENFQRQAVMNSAL
ParentalRQMSYGGKFGSSPLDQSGFSPSVQSHSHSFNQSSSSQWRQGTPSSQRKVRMNSYPYLADRHYSREQRYTD
RQMSYGGKF.SSPLDQSGFSPSVQSHSHSFNQSSSSQWRQGTPSSQRKVRMNS.PYLADRHYSREQRYTD
RetrocopyRQMSYGGKFASSPLDQSGFSPSVQSHSHSFNQSSSSQWRQGTPSSQRKVRMNSHPYLADRHYSREQRYTD
ParentalHGSDHHYRGKR-DDFFYEDRNHDDWSHDYDNRRDSSRDGKWRSSRH
HGSDHHYRGKR.D.F.YEDRNHD.WSHDYDNRRDSSRDGKWRSSRH
RetrocopyHGSDHHYRGKR>DFF-YEDRNHDGWSHDYDNRRDSSRDGKWRSSRH

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 29 .00 RPM
bodymap2_adrenal 0 .04 RPM 27 .51 RPM
bodymap2_brain 0 .02 RPM 12 .68 RPM
bodymap2_breast 0 .02 RPM 30 .06 RPM
bodymap2_colon 0 .00 RPM 38 .46 RPM
bodymap2_heart 0 .00 RPM 14 .64 RPM
bodymap2_kidney 0 .00 RPM 32 .88 RPM
bodymap2_liver 0 .00 RPM 14 .20 RPM
bodymap2_lung 0 .00 RPM 47 .27 RPM
bodymap2_lymph_node 0 .00 RPM 31 .36 RPM
bodymap2_ovary 0 .00 RPM 51 .82 RPM
bodymap2_prostate 0 .00 RPM 39 .35 RPM
bodymap2_skeletal_muscle 0 .00 RPM 17 .70 RPM
bodymap2_testis 0 .02 RPM 37 .39 RPM
bodymap2_thyroid 0 .08 RPM 28 .08 RPM
bodymap2_white_blood_cells 0 .02 RPM 35 .20 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_2283 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2283 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_125509492 libraries 552 libraries 658 libraries 103 libraries 24 libraries

The graphical summary, for retro_hsap_2283 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_2283 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2283 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1617
Gorilla gorilla retro_ggor_1696
Parental genes homology:
Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000135141 retrocopy
retro_cfam_1021,
Choloepus hoffmanni ENSCHOG000000127471 retrocopy
retro_chof_570,
Homo sapiens ENSG00000076053 1 retrocopy
retro_hsap_2283 ,
Homo sapiens ENSG000001433681 retrocopy
retro_hsap_1356,
Gorilla gorilla ENSGGOG000000099411 retrocopy
retro_ggor_1696,
Loxodonta africana ENSLAFG000000124441 retrocopy
retro_lafr_892,
Myotis lucifugus ENSMLUG000000232342 retrocopies
retro_mluc_1555, retro_mluc_587,
Monodelphis domestica ENSMODG000000139181 retrocopy
retro_mdom_535,
Mus musculus ENSMUSG000000423961 retrocopy
retro_mmus_2436,
Nomascus leucogenys ENSNLEG000000073231 retrocopy
retro_nleu_409,
Oryctolagus cuniculus ENSOCUG000000033421 retrocopy
retro_ocun_924,
Otolemur garnettii ENSOGAG000000168571 retrocopy
retro_ogar_3103,
Pongo abelii ENSPPYG000000038941 retrocopy
retro_pabe_1669,
Pan troglodytes ENSPTRG000000043051 retrocopy
retro_ptro_1617,
Ictidomys tridecemlineatus ENSSTOG000000124591 retrocopy
retro_itri_889,
Tursiops truncatus ENSTTRG000000015153 retrocopies
retro_ttru_1316, retro_ttru_1441, retro_ttru_478,
Vicugna pacos ENSVPAG000000063001 retrocopy
retro_vpac_311,

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 = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .03 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 .09 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 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 .03 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 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).



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