RetrogeneDB ID:

retro_hsap_3152

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:24170479..24171151(+)
Located in intron of:ENSG00000248874
Retrocopy
information
Ensembl ID:ENSG00000226432
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:AKTIP
Ensembl ID:ENSG00000166971
Aliases:AKTIP, FT1, FTS
Description:AKT interacting protein [Source:HGNC Symbol;Acc:16710]


Retrocopy-Parental alignment summary:






>retro_hsap_3152
ATGAACCCTTTCTGGAGCATGTCTACAAGCTCTGTACACAAACGATCTGAAGGTGAAGAGAAGACATTAACAGGGGACGT
GAAAACCAGTCCTCCACGAACTGCACCAAAGAAACAGCTGCCTTCTATTCCCAAAAATGCTTTGCCCATAACTAAGCCTA
CATCTCCTGCCCCAGCAGCACAGTCAACAAATGGCACGCATGCGTCCTATGGACCCTTCTACCTGGAATACTCTCTTCTT
GCAGAATTTACCTTGGTTGTGAAGCAGAAGCTACCAGGCGTCTATGTGCAGCCATCTTATCGCTCTGCATTAATGTGGTT
TGGAGTAATATTCATACAGCATGGACTTTACCAAGATGGCGTATTTAAGTTTACAGTTTACATCCCTGATAACTATCCAG
ATGGTGACTGTCCACGCTTGGTGTTCGATATTCCTGTCTTTCACCCGCTAGTTGATCCCACCTCAGGTGAGCTGGACGTG
AAGAGAGCATTTGCAAAATGGAGGCGGAACCATAATCATATTTGGTAGGTATTAATGTATGCAAGGAGAGTTTTCTACAA
GATTGATACAGCAAGCCCCCTGAACCCAGAGGCTGCAGTACTGTATGAAAAAGATATTCAGCTTTTTAAAAGTAAAGTTG
TTGACAGTGTTAAGGTGTGCACTGCTCGTTTG

ORF - retro_hsap_3152 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.66 %
Parental protein coverage: 76.71 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNPFWSMSTSSVRKRSEGEEKTLTGDVKTSPPRTAPKKQLPSIPKNALPITKPTSPAPAAQSTNGTHASY
MNPFWSMSTSSV.KRSEGEEKTLTGDVKTSPPRTAPKKQLPSIPKNALPITKPTSPAPAAQSTNGTHASY
RetrocopyMNPFWSMSTSSVHKRSEGEEKTLTGDVKTSPPRTAPKKQLPSIPKNALPITKPTSPAPAAQSTNGTHASY
ParentalGPFYLEYSLLAEFTLVVKQKLPGVYVQPSYRSALMWFGVIFIRHGLYQDGVFKFTVYIPDNYPDGDCPRL
GPFYLEYSLLAEFTLVVKQKLPGVYVQPSYRSALMWFGVIFI.HGLYQDGVFKFTVYIPDNYPDGDCPRL
RetrocopyGPFYLEYSLLAEFTLVVKQKLPGVYVQPSYRSALMWFGVIFIQHGLYQDGVFKFTVYIPDNYPDGDCPRL
ParentalVFDIPVFHPLVDPTSGELDVKRAFAKWRRNHNHIWQVLMYARRVFYKIDTASPLNPEAAVLYEKDIQLFK
VFDIPVFHPLVDPTSGELDVKRAFAKWRRNHNHIW.VLMYARRVFYKIDTASPLNPEAAVLYEKDIQLFK
RetrocopyVFDIPVFHPLVDPTSGELDVKRAFAKWRRNHNHIW*VLMYARRVFYKIDTASPLNPEAAVLYEKDIQLFK
ParentalSKVVDSVKVCTARL
SKVVDSVKVCTARL
RetrocopySKVVDSVKVCTARL

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 .02 RPM
bodymap2_adrenal 0 .00 RPM 11 .54 RPM
bodymap2_brain 0 .05 RPM 30 .33 RPM
bodymap2_breast 0 .02 RPM 12 .76 RPM
bodymap2_colon 0 .04 RPM 14 .71 RPM
bodymap2_heart 0 .00 RPM 22 .97 RPM
bodymap2_kidney 0 .06 RPM 15 .49 RPM
bodymap2_liver 0 .00 RPM 5 .72 RPM
bodymap2_lung 0 .00 RPM 8 .47 RPM
bodymap2_lymph_node 0 .00 RPM 13 .98 RPM
bodymap2_ovary 0 .02 RPM 19 .06 RPM
bodymap2_prostate 0 .09 RPM 15 .90 RPM
bodymap2_skeletal_muscle 0 .05 RPM 12 .84 RPM
bodymap2_testis 0 .15 RPM 30 .88 RPM
bodymap2_thyroid 0 .00 RPM 19 .62 RPM
bodymap2_white_blood_cells 0 .00 RPM 11 .54 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3152 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_3152 retrocopy
EST ID Start End Identity Match Mis-match Score
CB126446 24170566 24170810 99.2 242 2 240

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_1533611792 libraries32 libraries2 libraries3 libraries0 libraries

The graphical summary, for retro_hsap_3152 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_3152 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3152 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2282
Parental genes homology:
Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000163451 retrocopy
retro_amel_392,
Canis familiaris ENSCAFG000000095001 retrocopy
retro_cfam_1826,
Choloepus hoffmanni ENSCHOG000000136902 retrocopies
retro_chof_2533, retro_chof_629,
Callithrix jacchus ENSCJAG000000014981 retrocopy
retro_cjac_2895,
Cavia porcellus ENSCPOG000000065231 retrocopy
retro_cpor_622,
Dasypus novemcinctus ENSDNOG000000049064 retrocopies
retro_dnov_1376, retro_dnov_1776, retro_dnov_2080, retro_dnov_756,
Equus caballus ENSECAG000000203811 retrocopy
retro_ecab_504,
Homo sapiens ENSG00000166971 2 retrocopies
retro_hsap_1458, retro_hsap_3152 ,
Gorilla gorilla ENSGGOG000000148211 retrocopy
retro_ggor_1122,
Microcebus murinus ENSMICG000000108103 retrocopies
retro_mmur_124, retro_mmur_333, retro_mmur_985,
Microcebus murinus ENSMICG000000167931 retrocopy
retro_mmur_1191,
Monodelphis domestica ENSMODG000000257881 retrocopy
retro_mdom_1881,
Nomascus leucogenys ENSNLEG000000011061 retrocopy
retro_nleu_2660,
Otolemur garnettii ENSOGAG000000144951 retrocopy
retro_ogar_365,
Oryzias latipes ENSORLG000000137471 retrocopy
retro_olat_30,
Pongo abelii ENSPPYG000000073512 retrocopies
retro_pabe_1204, retro_pabe_1205,
Pan troglodytes ENSPTRG000000081161 retrocopy
retro_ptro_2282,
Rattus norvegicus ENSRNOG000000119561 retrocopy
retro_rnor_1611,
Tupaia belangeri ENSTBEG000000171055 retrocopies
retro_tbel_1063, retro_tbel_2864, retro_tbel_3350, retro_tbel_4130, retro_tbel_853,
Tursiops truncatus ENSTTRG000000127051 retrocopy
retro_ttru_348,

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 = 0.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 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 .08 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 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).





Copyright © RetrogeneDB 2014-2017