RetrogeneDB ID:

retro_hsap_3387

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:132323346..132323802(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229738
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRNP27
Ensembl ID:ENSG00000124380
Aliases:None
Description:small nuclear ribonucleoprotein 27kDa (U4/U6.U5) [Source:HGNC Symbol;Acc:30240]


Retrocopy-Parental alignment summary:






>retro_hsap_3387
ATGGGTGGCAGTCGCAGCGGCTCCCCACGGAGGAAAGGTAGGCGTTCCCGGTCCACATCCCGTGAGAGAGAACGCAGGCT
CCAAGAAAGGTCCAGGTCTCGGGAGAGAGATGGGAGAAGGAACCGCTCGCCAACCCCGCACCTAGGACGCTCCCGATCTC
CAAGACGACATAAATCCACATCTCCTTCCCCTTCTCAGCCGAACGAAAGAAGAGATGAGGAAAAGAAAGAAACAAAGAGC
AAAGAATGGCAAATTACTGAGGAAGACTTAGAGGGCAAAACAGAGGAAGAAATAGAAATGATGAAGTTAATGGAATTTGT
CTCCTTTGACTCCACAAAAGGTGAGAAGGTGGATTGCTCTGTAAATGCCTATGCCATAATTGTCTCTCAGAAGAGGAAGT
ACGGGCAGTAGATGAATCGAAAAGGTGGATTCCACAGACCTTTGGATTTCATTGCA

ORF - retro_hsap_3387 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.94 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGRSRSRSPRRERRRSRSTSRERERRRRERSRSRERDRRRSRSRSPHRRRSRSPRRHRSTSPSPSRLKER
MG.SRS.SPRR..RRSRSTSRERERR..ERSRSRERD.RR.RS..PH..RSRSPRRH.STSPSPS...ER
RetrocopyMGGSRSGSPRRKGRRSRSTSRERERRLQERSRSRERDGRRNRSPTPHLGRSRSPRRHKSTSPSPSQPNER
ParentalRDEEKKETKETKSKERQITEEDLEGKTEEEIEMMKLMGFASFDSTKGKKVDGSVNAYAINVSQKRKYRQY
RDEEK...KETKSKE.QITEEDLEGKTEEEIEMMKLM.F.SFDSTKG.KVD.SVNAYAI.VSQKRKY.Q.
RetrocopyRDEEK---KETKSKEWQITEEDLEGKTEEEIEMMKLMEFVSFDSTKGEKVDCSVNAYAIIVSQKRKYGQ*
ParentalMNRKGGFNRPLDFIA
MNRKGGF.RPLDFIA
RetrocopyMNRKGGFHRPLDFIA

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 24 .97 RPM
bodymap2_adrenal 0 .00 RPM 22 .54 RPM
bodymap2_brain 0 .00 RPM 33 .36 RPM
bodymap2_breast 0 .00 RPM 27 .51 RPM
bodymap2_colon 0 .00 RPM 29 .51 RPM
bodymap2_heart 0 .00 RPM 23 .08 RPM
bodymap2_kidney 0 .00 RPM 24 .46 RPM
bodymap2_liver 0 .00 RPM 11 .01 RPM
bodymap2_lung 0 .00 RPM 30 .19 RPM
bodymap2_lymph_node 0 .00 RPM 30 .92 RPM
bodymap2_ovary 0 .00 RPM 16 .94 RPM
bodymap2_prostate 0 .00 RPM 29 .55 RPM
bodymap2_skeletal_muscle 0 .00 RPM 32 .90 RPM
bodymap2_testis 0 .00 RPM 24 .19 RPM
bodymap2_thyroid 0 .00 RPM 25 .01 RPM
bodymap2_white_blood_cells 0 .00 RPM 28 .37 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3387 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3387 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_148701917 libraries803 libraries106 libraries3 libraries0 libraries

The graphical summary, for retro_hsap_3387 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_3387 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3387 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2300
Pongo abelii retro_pabe_2782
Parental genes homology:
Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000377464 retrocopies
retro_btau_1352, retro_btau_375, retro_btau_514, retro_btau_515,
Choloepus hoffmanni ENSCHOG000000030421 retrocopy
retro_chof_2589,
Echinops telfairi ENSETEG000000173441 retrocopy
retro_etel_655,
Homo sapiens ENSG00000124380 1 retrocopy
retro_hsap_3387 ,
Mus musculus ENSMUSG000000011582 retrocopies
retro_mmus_1977, retro_mmus_2105,
Oryctolagus cuniculus ENSOCUG000000229671 retrocopy
retro_ocun_1281,
Pongo abelii ENSPPYG000000123322 retrocopies
retro_pabe_1990, retro_pabe_2782,
Pan troglodytes ENSPTRG000000120221 retrocopy
retro_ptro_2300,
Sus scrofa ENSSSCG000000256741 retrocopy
retro_sscr_285,

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 .03 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 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 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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