RetrogeneDB ID:

retro_hsap_2141

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:110941632..110942241(+)
Located in intron of:ENSG00000144061
Retrocopy
information
Ensembl ID:ENSG00000233370
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTR1A
Ensembl ID:ENSG00000138107
Aliases:ACTR1A, ARP1, CTRN1
Description:ARP1 actin-related protein 1 homolog A, centractin alpha (yeast) [Source:HGNC Symbol;Acc:167]


Retrocopy-Parental alignment summary:






>retro_hsap_2141
GTGGAGTCTTACGATACAATCACCAACCAGCCTGTCATGATCGACAATGAATCTGGTGTGATTAAAGCTGGTTTTGCTGG
TGATCAGATCCACAAATACTGCTTTCCAAAGTATGTGGGCCTACCCATGCATATTCGTATCATGGCAGGAGCCCTTGAAG
GTGACATCTTCATTGGCTTCAAAGCCAAGGAGCACCAAGGGCTGCTCTCAATCTGCTATCTCACGGAGCATGGCATTGTC
AAGGACTGGAACGACATGGAACACATCTGGCAATATGTCTATTCTAAGGACCAGCTGCAGACTTTCTCAGAGGAGCATCT
CGTGCTCCTCACTGAGGCACCTTTAAACCCACAAAGACACCAGGAATGAGCTGCCAACGTTTTCTTCAAGAGCTTCAATG
TGCCTGCTATTTTCATCTCCATGTAAGCTGTGCTCAGCCTTTATGCCACAGGCAGGACCACGGGGGTGGTGCTGGATTCT
GGGGATGGCATCACCCATGCTGTGCCCATCTATCAGGGCTTTGCCATGCCCCACTCCATCATGCGAATTGACATCGCAAG
CTGGAACATCTCTCGCTTCCTGCACCTCTACCTGCATAAGGAGGGCTAT

ORF - retro_hsap_2141 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.77 %
Parental protein coverage: 53.99 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMESYDVIANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGPKAEEHRGLLS
.ESYD.I.NQPV.IDN.SGVIKAGFAGDQI.KYCFP.YVG.P.H.R.MAGALEGDIFIG.KA.EH.GLLS
RetrocopyVESYDTITNQPVMIDNESGVIKAGFAGDQIHKYCFPKYVGLPMHIRIMAGALEGDIFIGFKAKEHQGLLS
ParentalIRYPMEHGIVKDWNDMERIWQYVYSKDQLQTFSEEHPVLLTEAPLNPRKNRERAAEVFFETFNVPALFIS
I.Y..EHGIVKDWNDME.IWQYVYSKDQLQTFSEEH.VLLTEAPLNP....E.AA.VFF..FNVPA.FIS
RetrocopyICYLTEHGIVKDWNDMEHIWQYVYSKDQLQTFSEEHLVLLTEAPLNPQRHQE*AANVFFKSFNVPAIFIS
ParentalMQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSIMRIDIAGRDVSRFLRLYLRKEGY
M.AVLSLYATGRTTGVVLDSGDG.THAVPIY.GFAMPHSIMRIDIA....SRFL.LYL.KEGY
RetrocopyM*AVLSLYATGRTTGVVLDSGDGITHAVPIYQGFAMPHSIMRIDIASWNISRFLHLYLHKEGY

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 104 .38 RPM
bodymap2_adrenal 0 .00 RPM 76 .80 RPM
bodymap2_brain 0 .00 RPM 107 .80 RPM
bodymap2_breast 0 .00 RPM 81 .93 RPM
bodymap2_colon 0 .00 RPM 82 .14 RPM
bodymap2_heart 0 .00 RPM 75 .32 RPM
bodymap2_kidney 0 .00 RPM 84 .25 RPM
bodymap2_liver 0 .00 RPM 39 .76 RPM
bodymap2_lung 0 .00 RPM 122 .75 RPM
bodymap2_lymph_node 0 .00 RPM 99 .48 RPM
bodymap2_ovary 0 .00 RPM 65 .95 RPM
bodymap2_prostate 0 .12 RPM 147 .91 RPM
bodymap2_skeletal_muscle 0 .00 RPM 255 .50 RPM
bodymap2_testis 0 .11 RPM 93 .70 RPM
bodymap2_thyroid 0 .00 RPM 62 .82 RPM
bodymap2_white_blood_cells 0 .00 RPM 104 .09 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2141 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2141 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2141 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2141 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2141 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1567
Pongo abelii retro_pabe_1930
Parental genes homology:
Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000756246 retrocopies
retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Homo sapiens ENSG00000138107 1 retrocopy
retro_hsap_2141 ,
Homo sapiens ENSG0000018400910 retrocopies
retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Mus musculus ENSMUSG000000252281 retrocopy
retro_mmus_2686,
Nomascus leucogenys ENSNLEG000000151571 retrocopy
retro_nleu_2751,
Pongo abelii ENSPPYG000000026051 retrocopy
retro_pabe_1930,
Pan troglodytes ENSPTRG000000028941 retrocopy
retro_ptro_1567,
Drosophila melanogaster FBgn00117451 retrocopy
retro_dmel_80,

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 = 0.05 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 .05 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 .04 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 .00 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 .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 .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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