RetrogeneDB ID:

retro_hsap_302

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:211380580..211381237(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226986
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PRELID1
Ensembl ID:ENSG00000169230
Aliases:PRELID1, PRELI, PX19, SBBI12
Description:PRELI domain containing 1 [Source:HGNC Symbol;Acc:30255]


Retrocopy-Parental alignment summary:






>retro_hsap_302
ATGGTGAAGTATTTCCTGGGCCAGAGCGTGCAACGGAGCTCCTGGGACCAAGTGTTCGCCGCCTTCTGGCAGCGGTACCC
GAATCCCTATAGCAAACATGTCTTGACGGAAGACGTAGTACACCGGGAGGTAACCCCTGACCAGAAACTGCTGTCCGGGC
GACTCCTGACCAAGACCAACAGGACGCCCTGCTGGGCCGAGCGACTGTTTCCTGCCAATGTTGATCACTCGGTGTACATC
CTGGAGGACTCTATTGTGGACCCACAGAATCAGACCATGACCACCTTCACCTGGAACATCAACCATGCCCGGCTGATGGT
GGTGGAGGAACGATGTGTTTACTGTGTGAACTCTGACAACAGTGGCCGGACCGAAATCCGCCGGGAAGCCTGGGTCTCCT
CTAGCTTATTTGGTGTCTCCAGAGCTGTCCAGGAATTTGGTCTTGCCTGGTTCAAAAGCAATGTGACCAAGACTATGAAG
GGTTTTGAATATATCTTGGCAAAGCTGCAAGGCGAGGCCCCTTCCAAAACACTTGTTGAGACAGCCAAGGAAGCCAAGGA
GAAGGCAAAGGAGACAGCACTGGCAGCTACAGAGAAGGCCAAGGACCTCGCCAGCAAGGCAGCCACCAAGAAGCAGCAGC
AGCAGCAACAGTTTGTG

ORF - retro_hsap_302 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.89 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVKYFLGQSVLRSSWDQVFAAFWQRYPNPYSKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERLF
MVKYFLGQSV.RSSWDQVFAAFWQRYPNPYSKHVLTED.VHREVTPDQKLLS.RLLTKTNR.P.WAERLF
RetrocopyMVKYFLGQSVQRSSWDQVFAAFWQRYPNPYSKHVLTEDVVHREVTPDQKLLSGRLLTKTNRTPCWAERLF
ParentalPANVAHSVYVLEDSIVDPQNQTMTTFTWNINHARLMVVEERCVYCVNSDNSGWTEIRREAWVSSSLFGVS
PANV.HSVY.LEDSIVDPQNQTMTTFTWNINHARLMVVEERCVYCVNSDNSG.TEIRREAWVSSSLFGVS
RetrocopyPANVDHSVYILEDSIVDPQNQTMTTFTWNINHARLMVVEERCVYCVNSDNSGRTEIRREAWVSSSLFGVS
ParentalRAVQEFGLARFKSNVTKTMKGFEYILAKLQGEAPSKTLVETAKEAKEKAKETALAATEKAKDLASKAATK
RAVQEFGLA.FKSNVTKTMKGFEYILAKLQGEAPSKTLVETAKEAKEKAKETALAATEKAKDLASKAATK
RetrocopyRAVQEFGLAWFKSNVTKTMKGFEYILAKLQGEAPSKTLVETAKEAKEKAKETALAATEKAKDLASKAATK
ParentalKQQQQQQFV
KQQQQQQFV
RetrocopyKQQQQQQFV

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 .02 RPM 16 .04 RPM
bodymap2_adrenal 0 .31 RPM 27 .14 RPM
bodymap2_brain 0 .02 RPM 7 .29 RPM
bodymap2_breast 0 .02 RPM 12 .43 RPM
bodymap2_colon 0 .00 RPM 15 .29 RPM
bodymap2_heart 0 .00 RPM 3 .71 RPM
bodymap2_kidney 0 .04 RPM 15 .65 RPM
bodymap2_liver 0 .02 RPM 15 .27 RPM
bodymap2_lung 0 .11 RPM 19 .06 RPM
bodymap2_lymph_node 0 .00 RPM 17 .60 RPM
bodymap2_ovary 0 .06 RPM 12 .57 RPM
bodymap2_prostate 0 .03 RPM 14 .39 RPM
bodymap2_skeletal_muscle 0 .05 RPM 3 .46 RPM
bodymap2_testis 0 .00 RPM 13 .71 RPM
bodymap2_thyroid 0 .08 RPM 11 .96 RPM
bodymap2_white_blood_cells 0 .20 RPM 43 .08 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_302 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_302 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_302 retrocopy 5' end.

Lab - click to see more details

retro_hsap_302 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_302 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_9
Pongo abelii retro_pabe_377
Parental genes homology:
Parental genes homology involve 16 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000050092 retrocopies
retro_btau_1727, retro_btau_962,
Canis familiaris ENSCAFG000000164432 retrocopies
retro_cfam_2055, retro_cfam_349,
Callithrix jacchus ENSCJAG000000069535 retrocopies
retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Homo sapiens ENSG00000169230 7 retrocopies
retro_hsap_1550, retro_hsap_2269, retro_hsap_249, retro_hsap_302 , retro_hsap_3518, retro_hsap_3565, retro_hsap_579,
Gorilla gorilla ENSGGOG000000117623 retrocopies
retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Macropus eugenii ENSMEUG0000000173812 retrocopies
retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus ENSMLUG000000070082 retrocopies
retro_mluc_239, retro_mluc_64,
Macaca mulatta ENSMMUG000000090462 retrocopies
retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica ENSMODG000000048043 retrocopies
retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mustela putorius furoENSMPUG000000122261 retrocopy
retro_mputfur_579,
Nomascus leucogenys ENSNLEG000000127145 retrocopies
retro_nleu_1382, retro_nleu_2395, retro_nleu_2400, retro_nleu_803, retro_nleu_857,
Otolemur garnettii ENSOGAG000000114554 retrocopies
retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Pongo abelii ENSPPYG000000160867 retrocopies
retro_pabe_1283, retro_pabe_1696, retro_pabe_1699, retro_pabe_2907, retro_pabe_377, retro_pabe_409, retro_pabe_608,
Sus scrofa ENSSSCG000000140424 retrocopies
retro_sscr_372, retro_sscr_794, retro_sscr_795, retro_sscr_811,
Tupaia belangeri ENSTBEG000000064451 retrocopy
retro_tbel_3855,
Tursiops truncatus ENSTTRG000000095711 retrocopy
retro_ttru_1886,

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 = 0.18 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .18 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .12 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .17 RPM
GBR_HG00099 0 .09 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .14 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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