RetrogeneDB ID:

retro_hsap_400

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:64308864..64309347(-)
Located in intron of:ENSG00000185483
Retrocopy
information
Ensembl ID:ENSG00000228056
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CFL1
Ensembl ID:ENSG00000172757
Aliases:CFL1, CFL, HEL-S-15
Description:cofilin 1 (non-muscle) [Source:HGNC Symbol;Acc:1874]


Retrocopy-Parental alignment summary:






>retro_hsap_400
GTGTGGCTGTCTGATGGTGTCATGAACATGTTCAACGACATGAAGTTGCATAAGTCTTCAATGCCAGAGGAGGTGAAGAA
GCTCAAGAAGGTGGTGCTCTTCTGCCTTAGTGAGGACAAGAAGAACATCATCCTGGAGGAGACCAAGAAGATCCTGGTGG
GCGATGTGAGCCAGACCATCGACGACCCCTACACCACCTTTGTCAGGATGCTGCCAGATAAGGACTGCCACTACACCCTC
TGTGACACAACCTACGAGACCAAGGAGAGCAAGGAGGAGGACCTGGTGTTTATCTTCTGGGTCCCTGAGTCTGCTCCCCT
TAAAAGCAAAATGATCTATGCCAGCTCCAAGGACGCCGTCAAGAAGCTGACAGGGATCAAGCATGAATTACACACAAACT
GCTACAAGGAGGTCAAGGACCGCTGCACCCTGGCAGAGAAGCTGGGGGGCAGTGCGGTCATCTCCCTAGAGGACAAGCCT
TTG

ORF - retro_hsap_400 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.72 %
Parental protein coverage: 97.59 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVGQTVDDPYATFVKM
V..SDGV...FNDMK..KSS.PEEVKK.KK.VLFCLSEDKKNIILEE.K.ILVGDV.QT.DDPY.TFV.M
RetrocopyVWLSDGVMNMFNDMKLHKSSMPEEVKKLKKVVLFCLSEDKKNIILEETKKILVGDVSQTIDDPYTTFVRM
ParentalLPDKDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKLTGIKHELQANCYEEVK
LPDKDC.Y.L.D.TYETKESK.EDLVFIFW.PESAPLKSKMIYASSKDA.KK.LTGIKHEL..NCY.EVK
RetrocopyLPDKDCHYTLCDTTYETKESKEEDLVFIFWVPESAPLKSKMIYASSKDAVKK-LTGIKHELHTNCYKEVK
ParentalDRCTLAEKLGGSAVISLEGKPL
DRCTLAEKLGGSAVISLE.KPL
RetrocopyDRCTLAEKLGGSAVISLEDKPL

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 .04 RPM 357 .29 RPM
bodymap2_adrenal 0 .00 RPM 443 .33 RPM
bodymap2_brain 0 .00 RPM 248 .63 RPM
bodymap2_breast 0 .00 RPM 215 .18 RPM
bodymap2_colon 0 .00 RPM 251 .77 RPM
bodymap2_heart 0 .02 RPM 129 .43 RPM
bodymap2_kidney 0 .00 RPM 272 .71 RPM
bodymap2_liver 0 .00 RPM 182 .09 RPM
bodymap2_lung 0 .00 RPM 512 .10 RPM
bodymap2_lymph_node 0 .00 RPM 360 .10 RPM
bodymap2_ovary 0 .00 RPM 214 .98 RPM
bodymap2_prostate 0 .00 RPM 284 .97 RPM
bodymap2_skeletal_muscle 0 .00 RPM 64 .60 RPM
bodymap2_testis 0 .04 RPM 209 .61 RPM
bodymap2_thyroid 0 .00 RPM 173 .89 RPM
bodymap2_white_blood_cells 0 .00 RPM 780 .01 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_400 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_400 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_96047395 libraries699 libraries703 libraries30 libraries2 libraries

The graphical summary, for retro_hsap_400 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_400 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_400 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_306
Gorilla gorilla retro_ggor_397
Pongo abelii retro_pabe_316
Parental genes homology:
Parental genes homology involve 19 parental genes, and 73 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000173342 retrocopies
retro_amel_583, retro_amel_816,
Canis familiaris ENSCAFG000000249556 retrocopies
retro_cfam_1544, retro_cfam_366, retro_cfam_660, retro_cfam_67, retro_cfam_943, retro_cfam_964,
Callithrix jacchus ENSCJAG000000019161 retrocopy
retro_cjac_347,
Equus caballus ENSECAG000000199001 retrocopy
retro_ecab_442,
Felis catus ENSFCAG000000132723 retrocopies
retro_fcat_1456, retro_fcat_303, retro_fcat_991,
Homo sapiens ENSG000001258681 retrocopy
retro_hsap_952,
Homo sapiens ENSG00000172757 6 retrocopies
retro_hsap_2617, retro_hsap_287, retro_hsap_3333, retro_hsap_336, retro_hsap_384, retro_hsap_400 ,
Gorilla gorilla ENSGGOG000000231835 retrocopies
retro_ggor_1832, retro_ggor_326, retro_ggor_357, retro_ggor_389, retro_ggor_397,
Myotis lucifugus ENSMLUG000000246856 retrocopies
retro_mluc_1905, retro_mluc_2114, retro_mluc_216, retro_mluc_2218, retro_mluc_455, retro_mluc_507,
Macaca mulatta ENSMMUG000000190165 retrocopies
retro_mmul_316, retro_mmul_493, retro_mmul_556, retro_mmul_667, retro_mmul_705,
Mustela putorius furoENSMPUG000000115022 retrocopies
retro_mputfur_1485, retro_mputfur_575,
Nomascus leucogenys ENSNLEG000000058525 retrocopies
retro_nleu_139, retro_nleu_1494, retro_nleu_1571, retro_nleu_1777, retro_nleu_636,
Oryctolagus cuniculus ENSOCUG000000256044 retrocopies
retro_ocun_1123, retro_ocun_1390, retro_ocun_324, retro_ocun_478,
Otolemur garnettii ENSOGAG000000165038 retrocopies
retro_ogar_1442, retro_ogar_1581, retro_ogar_1648, retro_ogar_2192, retro_ogar_302, retro_ogar_405, retro_ogar_453, retro_ogar_828,
Pongo abelii ENSPPYG000000030475 retrocopies
retro_pabe_1732, retro_pabe_2747, retro_pabe_316, retro_pabe_325, retro_pabe_386,
Pan troglodytes ENSPTRG000000038955 retrocopies
retro_ptro_1764, retro_ptro_2146, retro_ptro_236, retro_ptro_298, retro_ptro_306,
Rattus norvegicus ENSRNOG000000206602 retrocopies
retro_rnor_1354, retro_rnor_693,
Ictidomys tridecemlineatus ENSSTOG000000279684 retrocopies
retro_itri_144, retro_itri_1456, retro_itri_1734, retro_itri_685,
Tursiops truncatus ENSTTRG000000169312 retrocopies
retro_ttru_1256, retro_ttru_598,

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 .02 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 .03 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 .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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