RetrogeneDB ID:

retro_hsap_2205

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:208546313..208546754(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213082
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PPP1R14B
Ensembl ID:ENSG00000173457
Aliases:PPP1R14B, PHI-1, PLCB3N, PNG, SOM172
Description:protein phosphatase 1, regulatory (inhibitor) subunit 14B [Source:HGNC Symbol;Acc:9057]


Retrocopy-Parental alignment summary:






>retro_hsap_2205
ATGGCGGACAGCTGCACCGCGAGGGGCGTGGCGTTGGCTGCCCCGGACCCCGGGCAGGGCAGTGGCGGCCCAGGACAACG
CGTCTACTTTCAGAGCCCCCCTGGGCCGCAGGAGAGGGCCCGGGCGGCGCGGACGATGAGGGCCCAGTGAGGCGCCAAGT
GAAGGTCACCGTCAAGTATGACCGCAAGGAGCTACGGAAGCGCCTTAACCTAGAGGAGTGGATCCTGGAGCAGCTCACGC
GCCTCTACGACTGCCAGGAAGAGGAGATCCCAGAACTGGAAATTGACGTGGATGAGCTCCTGGACATGGAGAGTGACGAT
GCCCGTACTGCCAGGGTCAAGGAGCTGCTGGTTGACTTGTTACAAACCCACAGAGACCTTCATCTCTGGCCTGCTGGACA
AGATCCGGGGCATGCAGAAGCTGAGCACACCCCAGAAGAAG

ORF - retro_hsap_2205 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.62 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMADSGTAGGAALAAPAPGPGSGGPGPRVYFQSPPG-AAGEGPGGADDEGPVRRQGKVTVKYDRKELRKRL
MADS.TA.G.ALAAP.PG.GSGGPG.RVYFQSPPG.AAGEGPGGADDEGPVRRQ.KVTVKYDRKELRKRL
RetrocopyMADSCTARGVALAAPDPGQGSGGPGQRVYFQSPPG<AAGEGPGGADDEGPVRRQVKVTVKYDRKELRKRL
ParentalNLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDARAARVKELLVD-CYKPTEAFISGLLDKIRGM
NLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDAR.ARVKELLVD.CYKPTE.FISGLLDKIRGM
RetrocopyNLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDARTARVKELLVD>CYKPTETFISGLLDKIRGM
ParentalQKLSTPQKK
QKLSTPQKK
RetrocopyQKLSTPQKK

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 26 .60 RPM
bodymap2_adrenal 0 .02 RPM 34 .20 RPM
bodymap2_brain 0 .00 RPM 3 .75 RPM
bodymap2_breast 0 .00 RPM 20 .27 RPM
bodymap2_colon 0 .00 RPM 22 .35 RPM
bodymap2_heart 0 .00 RPM 13 .02 RPM
bodymap2_kidney 0 .06 RPM 30 .55 RPM
bodymap2_liver 0 .00 RPM 19 .14 RPM
bodymap2_lung 0 .00 RPM 18 .74 RPM
bodymap2_lymph_node 0 .02 RPM 21 .00 RPM
bodymap2_ovary 0 .00 RPM 20 .47 RPM
bodymap2_prostate 0 .00 RPM 21 .65 RPM
bodymap2_skeletal_muscle 0 .02 RPM 50 .42 RPM
bodymap2_testis 0 .17 RPM 17 .33 RPM
bodymap2_thyroid 0 .04 RPM 21 .19 RPM
bodymap2_white_blood_cells 0 .00 RPM 9 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2205 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2205 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2205 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2205 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2205 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1674
Parental genes homology:
Parental genes homology involve 7 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000181113 retrocopies
retro_cjac_3591, retro_cjac_428, retro_cjac_532,
Homo sapiens ENSG00000173457 4 retrocopies
retro_hsap_2205 , retro_hsap_3101, retro_hsap_3655, retro_hsap_3838,
Mustela putorius furoENSMPUG000000132082 retrocopies
retro_mputfur_235, retro_mputfur_798,
Nomascus leucogenys ENSNLEG000000048902 retrocopies
retro_nleu_324, retro_nleu_335,
Pan troglodytes ENSPTRG000000411386 retrocopies
retro_ptro_1674, retro_ptro_2097, retro_ptro_2480, retro_ptro_2614, retro_ptro_3089, retro_ptro_935,
Sus scrofa ENSSSCG000000130352 retrocopies
retro_sscr_1087, retro_sscr_892,
Ictidomys tridecemlineatus ENSSTOG000000219591 retrocopy
retro_itri_1110,

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 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .08 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 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 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 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .08 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 .00 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017