RetrogeneDB ID:

retro_hsap_1136

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:79187393..79187782(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000257564
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RALA
Ensembl ID:ENSG00000006451
Aliases:RALA, RAL
Description:v-ral simian leukemia viral oncogene homolog A (ras related) [Source:HGNC Symbol;Acc:9839]


Retrocopy-Parental alignment summary:






>retro_hsap_1136
AAAGAAGGCACCTATCGGAAGAGAGTAGTACTGGATGGCGAGGAAGTACAGATCGGTATCTTAGAAACAGCTGGGCAGGA
GGACTATGCTGCAATTAGGGACAACTATTTCCGAAGCAGAGAGGGGTTTCTCTGTGTCTTCTCTATTACAGAAATGGAAT
CCTTTGCAGCTACAGCTGACTTCAGGGAGCAGATTTTAAGAGTAAAAGAAGATGAGAATGTTCCATTTCTACTGGTTGGT
AACAAATCAGATTTAGAAGATAAAAGGCCGGTTTCTGTAAAAGAGGCAAAAAACAGAGCTGACCAGTGGAATGTTAACTA
TGTGGAAACATCTGCTAAAACACAGCTAATGTTGACAAGGTACTTTTTGATTTAATGAGAGAAATTCGA

ORF - retro_hsap_1136 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.08 %
Parental protein coverage: 63.11 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKE
K...YRK.VVLDGEEVQI.IL.TAGQEDYAAIRDNYFRS.EGFLCVFSITEMESFAATADFREQILRVKE
RetrocopyKEGTYRKRVVLDGEEVQIGILETAGQEDYAAIRDNYFRSREGFLCVFSITEMESFAATADFREQILRVKE
ParentalDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETSAKTR-ANVDKVFFDLMREIR
DENVPFLLVGNKSDLEDKR.VSV.EAKNRA.QWNVNYVETSAKT..ANVDKV.FDLMREIR
RetrocopyDENVPFLLVGNKSDLEDKRPVSVKEAKNRADQWNVNYVETSAKTQ<ANVDKVLFDLMREIR

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 62 .79 RPM
bodymap2_adrenal 0 .02 RPM 59 .71 RPM
bodymap2_brain 0 .00 RPM 52 .51 RPM
bodymap2_breast 0 .00 RPM 97 .34 RPM
bodymap2_colon 0 .00 RPM 73 .94 RPM
bodymap2_heart 0 .00 RPM 32 .51 RPM
bodymap2_kidney 0 .00 RPM 54 .04 RPM
bodymap2_liver 0 .00 RPM 18 .80 RPM
bodymap2_lung 0 .00 RPM 130 .63 RPM
bodymap2_lymph_node 0 .00 RPM 55 .66 RPM
bodymap2_ovary 0 .00 RPM 87 .00 RPM
bodymap2_prostate 0 .00 RPM 59 .41 RPM
bodymap2_skeletal_muscle 0 .00 RPM 24 .74 RPM
bodymap2_testis 0 .13 RPM 74 .88 RPM
bodymap2_thyroid 0 .00 RPM 49 .22 RPM
bodymap2_white_blood_cells 0 .00 RPM 65 .74 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1136 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1136 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1136 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1136 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1136 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_945
Macaca mulatta retro_mmul_882
Parental genes homology:
Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000076301 retrocopy
retro_cjac_3313,
Dasypus novemcinctus ENSDNOG000000174131 retrocopy
retro_dnov_573,
Homo sapiens ENSG00000006451 2 retrocopies
retro_hsap_1136 , retro_hsap_3707,
Homo sapiens ENSG000001164731 retrocopy
retro_hsap_1364,
Homo sapiens ENSG000001273142 retrocopies
retro_hsap_3338, retro_hsap_4234,
Homo sapiens ENSG000001337031 retrocopy
retro_hsap_3474,
Macropus eugenii ENSMEUG000000002591 retrocopy
retro_meug_1638,
Macaca mulatta ENSMMUG000000160592 retrocopies
retro_mmul_1706, retro_mmul_882,
Nomascus leucogenys ENSNLEG000000030551 retrocopy
retro_nleu_935,
Pongo abelii ENSPPYG000000176193 retrocopies
retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes ENSPTRG000000191081 retrocopy
retro_ptro_2511,
Sus scrofa ENSSSCG000000297411 retrocopy
retro_sscr_634,
Ictidomys tridecemlineatus ENSSTOG000000202922 retrocopies
retro_itri_1314, retro_itri_1315,
Vicugna pacos ENSVPAG000000028101 retrocopy
retro_vpac_211,

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 .02 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 .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 .02 RPM
YRI_NA19214 0 .02 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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