RetrogeneDB ID:

retro_hsap_3195

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:75672499..75672976(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000251235
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPC
Ensembl ID:ENSG00000124562
Aliases:None
Description:small nuclear ribonucleoprotein polypeptide C [Source:HGNC Symbol;Acc:11157]


Retrocopy-Parental alignment summary:






>retro_hsap_3195
ATGCCCAAGTTTTATTGTGACTACTGCAATACATACCTCACCCATGACTCTCCTCCTGTGAGAAAGACACACTGCAGTGG
TAGGAAACACAAAGAGAATGTGAAAGACTACTATCAGAAATGGATGAAAGAGCAGGCTCAGAGCCTGATTGACAAAACAA
CGGCTGCATTTCAACAAGGAAAGATACCTCCTGCTCCATTCTCTGCTCCTCCTCCTGTAGGAGCAATGATACCACCTCCC
CCTAGTCTTCCAGGTCCTCCTCACCCTGGTATGATGCCAGCACCCCATATGAGGGGTCCTGCCATGATGCCAATGATGGG
CCCTCCTCCTCCTGGGATGATGCCAGGGGGACCTGCTCCTGGAATGAGGCCGCTTATGGGAGGCCACAGGCCAATGATGC
CTGGGTCCCCAGTGATAAGACCTCCTGCCTGTCCCATGATGGTGCCCACTCGGCCCAGAAAGACTTGACCAGACAGA

ORF - retro_hsap_3195 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.68 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAP
MPKFYCDYC.TYLTHDSP.VRKTHCSGRKHKENVKDYYQKWM.EQAQSLIDKTTAAFQQGKIPP.PFSAP
RetrocopyMPKFYCDYCNTYLTHDSPPVRKTHCSGRKHKENVKDYYQKWMKEQAQSLIDKTTAAFQQGKIPPAPFSAP
ParentalPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGMRPPMGGHMPMMPGPPMMR
PP.GAMIPPPPSLPGPP.PGMMPAPHM.GP.MMPMMGPPPPGMMP.GPAPGMRP.MGGH.PMMPG.P..R
RetrocopyPPVGAMIPPPPSLPGPPHPGMMPAPHMRGPAMMPMMGPPPPGMMPGGPAPGMRPLMGGHRPMMPGSPVIR
ParentalPPARPMMVPTRPGMTRPDR
PPA.PMMVPTRP..T.PDR
RetrocopyPPACPMMVPTRPRKT*PDR

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 16 .28 RPM
bodymap2_adrenal 0 .00 RPM 31 .52 RPM
bodymap2_brain 0 .07 RPM 15 .14 RPM
bodymap2_breast 0 .00 RPM 17 .49 RPM
bodymap2_colon 0 .00 RPM 19 .55 RPM
bodymap2_heart 0 .00 RPM 37 .37 RPM
bodymap2_kidney 0 .00 RPM 21 .86 RPM
bodymap2_liver 0 .00 RPM 20 .30 RPM
bodymap2_lung 0 .00 RPM 18 .11 RPM
bodymap2_lymph_node 0 .00 RPM 26 .79 RPM
bodymap2_ovary 0 .00 RPM 20 .88 RPM
bodymap2_prostate 0 .00 RPM 32 .53 RPM
bodymap2_skeletal_muscle 0 .00 RPM 28 .50 RPM
bodymap2_testis 0 .00 RPM 49 .11 RPM
bodymap2_thyroid 0 .00 RPM 29 .04 RPM
bodymap2_white_blood_cells 0 .00 RPM 27 .72 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3195 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3195 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_15575527 libraries3 libraries103 libraries351 libraries1345 libraries

The graphical summary, for retro_hsap_3195 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_3195 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3195 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2249
Gorilla gorilla retro_ggor_1333
Parental genes homology:
Parental genes homology involve 11 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000245491 retrocopy
retro_btau_1636,
Canis familiaris ENSCAFG000000012313 retrocopies
retro_cfam_348, retro_cfam_402, retro_cfam_409,
Callithrix jacchus ENSCJAG0000001532116 retrocopies
retro_cjac_1009, retro_cjac_1015, retro_cjac_1064, retro_cjac_1750, retro_cjac_1937, retro_cjac_2014, retro_cjac_2395, retro_cjac_2456, retro_cjac_2785, retro_cjac_3056, retro_cjac_3110, retro_cjac_400, retro_cjac_4010, retro_cjac_617, retro_cjac_770, retro_cjac_873,
Homo sapiens ENSG00000124562 6 retrocopies
retro_hsap_1531, retro_hsap_1866, retro_hsap_2865, retro_hsap_3195 , retro_hsap_3829, retro_hsap_4241,
Loxodonta africana ENSLAFG000000135342 retrocopies
retro_lafr_621, retro_lafr_878,
Monodelphis domestica ENSMODG000000139041 retrocopy
retro_mdom_22,
Nomascus leucogenys ENSNLEG000000083922 retrocopies
retro_nleu_2129, retro_nleu_99,
Oryctolagus cuniculus ENSOCUG000000266683 retrocopies
retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii ENSOGAG000000087559 retrocopies
retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Pongo abelii ENSPPYG000000172724 retrocopies
retro_pabe_1271, retro_pabe_3066, retro_pabe_3225, retro_pabe_915,
Sarcophilus harrisii ENSSHAG000000009451 retrocopy
retro_shar_112,

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 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 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 .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 .00 RPM
GBR_HG00131 0 .03 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 .03 RPM
TSI_NA20513 0 .02 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 .09 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 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 .02 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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