RetrogeneDB ID:

retro_hsap_4301

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:112295737..112296540(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213539
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YBX1
Ensembl ID:ENSG00000065978
Aliases:YBX1, BP-8, CSDA2, CSDB, DBPB, MDR-NF1, NSEP-1, NSEP1, YB-1, YB1
Description:Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]


Retrocopy-Parental alignment summary:






>retro_hsap_4301
GACACCACGCCCGGCACTACGGGCAGCGGCACAGGAAACGGTGGCCCGGGAGGCTTCACATCAGCAGCACCTGCCGGCGG
GGACAAGAAGGTCATCGCAACGAAGGTTTTGGGAACAGTAAAATGGTTCAACTTAAGGAACGGATATGCTTTCATCAACA
GGAATGACATCAAGGAAGATACATTTGTACCCCAGACTGCCAAAACGAAGAATAACCCCAGGAGGTACCTTCGCAGTGTA
GAAATGGAGAGACTGTGGAGTTTGATGTGGTTGAAGGAGAAAAGGGTGCAGAGGCAGCACATGTTATAGGTCCTGGTGGT
GTTCCAGTTCAAGGCAGTAAACATGCAGCAGACCGTAACCCTTATAGATGCTATCCACGTCGTAGGGGTCCTCCACCCAA
TTACCAGCAAAACTACCAGAATAGCGAGAGTGGGGGAAAGAACGAGGGATGGGAGCGTGCTCCCCAAGGCCAGGCTCAAC
CACGCCGGCCCTACAGCAGGTGAAGGTTCCCACCTTCCTACATGCGGAGACCCTATGGGCGTGGACCACAGTATTCCAAC
CCTCCTGTGCAGGGAGAAGTGATGGAGGGTGCTGACAACCAGGGTGCAGGAAAACAAGGTAGATCAGTGTGGCAGAGTAT
ATATCAGGGATATAGACCACGATTCCGCAGGGGCCCTCCTCGCCAAAGACAGCCTAGAGAGGACGGCAATGAAGAGGATA
AAGAAAATCAACGAGGTGAGACCCAAGGTCAGCAGCCACCTCAACGTCGGTACCGCCGCAACTTACCGACGCAGACACAC
AGA

ORF - retro_hsap_4301 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.64 %
Parental protein coverage: 82.72 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDTKPGTTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKK
DT.PGTTGSG.G.GGPGG.TSAAPAGGDKKVIATKVLGTVKWFN.RNGY.FINRND.KED.FV.QTA..K
RetrocopyDTTPGTTGSGTGNGGPGGFTSAAPAGGDKKVIATKVLGTVKWFNLRNGYAFINRNDIKEDTFVPQTAKTK
ParentalNNPRKYLRSVG-DGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNY
NNPR.YLRSV...GETVEFDVVEGEKGAEAA.V.GPGGVPVQGSK.AADRN.YR.YPRRRGPP.NYQQNY
RetrocopyNNPRRYLRSVE<NGETVEFDVVEGEKGAEAAHVIGPGGVPVQGSKHAADRNPYRCYPRRRGPPPNYQQNY
ParentalQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGRP
QNSESG.KNEG.E.AP.GQAQ.RRPY.R.RFPP.YMRRPYGR.PQYSNPPVQGEVMEGADNQGAG.QGR.
RetrocopyQNSESGGKNEGWERAPQGQAQPRRPYSR*RFPPSYMRRPYGRGPQYSNPPVQGEVMEGADNQGAGKQGRS
ParentalVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRR
V.Q..Y.GYRPRFRRGPPRQRQPREDGNEEDKENQ..ETQGQQPPQRRYRRN......R
RetrocopyVWQSIYQGYRPRFRRGPPRQRQPREDGNEEDKENQRGETQGQQPPQRRYRRNLPTQTHR

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 808 .89 RPM
bodymap2_adrenal 0 .04 RPM 729 .35 RPM
bodymap2_brain 0 .00 RPM 92 .05 RPM
bodymap2_breast 0 .00 RPM 645 .42 RPM
bodymap2_colon 0 .08 RPM 666 .41 RPM
bodymap2_heart 0 .00 RPM 399 .44 RPM
bodymap2_kidney 0 .08 RPM 285 .62 RPM
bodymap2_liver 0 .00 RPM 200 .65 RPM
bodymap2_lung 0 .00 RPM 440 .84 RPM
bodymap2_lymph_node 0 .00 RPM 413 .70 RPM
bodymap2_ovary 0 .00 RPM 409 .27 RPM
bodymap2_prostate 0 .00 RPM 513 .49 RPM
bodymap2_skeletal_muscle 0 .13 RPM 1157 .31 RPM
bodymap2_testis 0 .02 RPM 1126 .79 RPM
bodymap2_thyroid 0 .00 RPM 666 .53 RPM
bodymap2_white_blood_cells 0 .02 RPM 398 .62 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4301 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4301 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4301 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4301 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4301 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3502
Macaca mulatta retro_mmul_1139
Parental genes homology:
Parental genes homology involve 20 parental genes, and 118 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000004949 retrocopies
retro_amel_1280, retro_amel_1358, retro_amel_141, retro_amel_1486, retro_amel_215, retro_amel_418, retro_amel_625, retro_amel_837, retro_amel_909,
Canis familiaris ENSCAFG000000025414 retrocopies
retro_cfam_1312, retro_cfam_2118, retro_cfam_758, retro_cfam_91,
Callithrix jacchus ENSCJAG000000031556 retrocopies
retro_cjac_1261, retro_cjac_1701, retro_cjac_2718, retro_cjac_3156, retro_cjac_4172, retro_cjac_817,
Cavia porcellus ENSCPOG000000108883 retrocopies
retro_cpor_654, retro_cpor_833, retro_cpor_905,
Felis catus ENSFCAG000000226046 retrocopies
retro_fcat_145, retro_fcat_1554, retro_fcat_1956, retro_fcat_241, retro_fcat_503, retro_fcat_631,
Homo sapiens ENSG000000060471 retrocopy
retro_hsap_637,
Homo sapiens ENSG000000601381 retrocopy
retro_hsap_1674,
Homo sapiens ENSG00000065978 4 retrocopies
retro_hsap_1433, retro_hsap_3886, retro_hsap_4250, retro_hsap_4301 ,
Loxodonta africana ENSLAFG000000075971 retrocopy
retro_lafr_804,
Microcebus murinus ENSMICG0000001498419 retrocopies
retro_mmur_1098, retro_mmur_1285, retro_mmur_1326, retro_mmur_1435, retro_mmur_1437, retro_mmur_1445, retro_mmur_1621, retro_mmur_199, retro_mmur_315, retro_mmur_413, retro_mmur_581, retro_mmur_640, retro_mmur_676, retro_mmur_679, retro_mmur_726, retro_mmur_837, retro_mmur_900, retro_mmur_919, retro_mmur_942,
Macaca mulatta ENSMMUG000000131365 retrocopies
retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Nomascus leucogenys ENSNLEG000000123247 retrocopies
retro_nleu_1053, retro_nleu_1188, retro_nleu_1312, retro_nleu_1601, retro_nleu_1749, retro_nleu_1888, retro_nleu_270,
Oryctolagus cuniculus ENSOCUG000000280472 retrocopies
retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii ENSOGAG0000000678425 retrocopies
retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Pongo abelii ENSPPYG000000014667 retrocopies
retro_pabe_1216, retro_pabe_1320, retro_pabe_2054, retro_pabe_2292, retro_pabe_3167, retro_pabe_3388, retro_pabe_3502,
Pteropus vampyrus ENSPVAG000000055047 retrocopies
retro_pvam_1255, retro_pvam_1348, retro_pvam_1391, retro_pvam_145, retro_pvam_405, retro_pvam_76, retro_pvam_971,
Sorex araneus ENSSARG000000078961 retrocopy
retro_sara_559,
Tarsius syrichta ENSTSYG000000069156 retrocopies
retro_tsyr_1030, retro_tsyr_173, retro_tsyr_2037, retro_tsyr_610, retro_tsyr_840, retro_tsyr_996,
Tursiops truncatus ENSTTRG000000013532 retrocopies
retro_ttru_461, retro_ttru_746,
Vicugna pacos ENSVPAG000000000682 retrocopies
retro_vpac_235, retro_vpac_647,

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 = 0.17 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .17 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .12 RPM
YRI_NA19214 0 .07 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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