RetrogeneDB ID:

retro_hsap_1674

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:31579707..31580818(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000261614
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YBX3
Ensembl ID:ENSG00000060138
Aliases:YBX3, CSDA, CSDA1, DBPA, ZONAB
Description:Y box binding protein 3 [Source:HGNC Symbol;Acc:2428]


Retrocopy-Parental alignment summary:






>retro_hsap_1674
ATGAGCGAGGCGGGCGAGGCCACCATCATCACCACCACCCTCCAGCAGGCTCCTGCGGTGGCGGCCGCCGCGGCTCCCCA
GGACCCCGCGACCAAGAGCCGGGTGGGCAGCGGTGCACCCCAAGCCGCGGCCCCGGCGCCCGCCGCCCTCGTCGCAGGAA
ACCCGGGTGGGGACGGGGCCCCCGCAGCCACGGGCACCGCGGCCGCCGCCTCTTTAGCCACCGCCGCCGACAGCGAAGAC
GCGGAGAAAAAAGTTCTCGCCACCAAAGTCCTTGGCACTGTCAAATGGTTCAACGTCAGAAATGGATATGGATTTATAAA
TCGAAATGACACCAAAGAAGATCTATTTATACATCAGACTGCCATCAAGAAGAATAACCCACAGAAATATCTGCGCAGTG
TAGGAGATGGAGAAACTGTAGAGTTTGATGTGGTTTAAGGAGAGAAGGGTGCAGAAGCAGCCAGTGTGACTGGCCGGGGT
GGAGTTCCTGTGGAGGGCAGTCGTTACGCGCTGATTGGCGCCGTTACAGACGTGGCTACTATGGAAGGCGCCATGGCCCT
CCCCGGGATTACGCTGGGAGGAGGAGGAAGAAGGGAGCGGCAGCAGTGAAGGATTTGACCCCCCTACCACTGATAGGCAG
TTCTCTGGGGCCCGGAATCGGCTGCGCCGCCCCCAGTATCGCCCCCAGTACAGGCAGCAGCGGTTCCCGCCTTACCACGT
GGGACAGACGTTTGACCGTCGCTCACCGGTCTTACCCCATCCCAACAGAATACAGGCTGTTGAGATTGGAGAGCTGAAGG
ATGGAGTCCCAGAAGGAGCACAACTTCAGGGACCATTTCATCGAAATCCAACTTACCGCCCAAGGTACCATAGCAGGGGA
CCTCCTCGCCCACGACCTGCCCCAGCAGTTGGAGAGGCTGAAGATAAAGAAAATCAGCAAGCCTCCAGTGGTCCAAACCA
GCCGCCTGTTCGCCGTGGATACCGGCGTCCCTACAATTACCGGCGTCGCCCACGTTCTCCTAACGCTCCTTCACAAGATG
GCAAAGAGGCCACGGCAGGTGAAGCACCAACTGAGAACCCTGCTCCATCCACCGAGCAGAGCAGTGCTGAG

ORF - retro_hsap_1674 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSEAGEATTTTTTTLPQAPTEAAAAAPQDPAPKSPVGSGAPQAAAPAPAAHVAGNPGGDAAPAATGTAAA
MSEAGEAT..TTT.L.QAP..AAAAAPQDPA.KS.VGSGAPQAAAPAPAA.VAGNPGGD.APAATGTAAA
RetrocopyMSEAGEATIITTT-LQQAPAVAAAAAPQDPATKSRVGSGAPQAAAPAPAALVAGNPGGDGAPAATGTAAA
ParentalASLATAAGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGET
ASLATAA.SEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKED.F.HQTAIKKNNP.KYLRSVGDGET
RetrocopyASLATAADSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDLFIHQTAIKKNNPQKYLRSVGDGET
ParentalVEFDVVEGEKGAEAANVTGPDGVPVEGSRYA-ADRRRYRRGYYGRRRGPPRNYAG-EEEEEGSGSSEGFD
VEFDVV.GEKGAEAA.VTG..GVPVEGSRYA.AD.RRYRRGYYGRR.GPPR.YAG.EEEEEGSGSSEGFD
RetrocopyVEFDVV*GEKGAEAASVTGRGGVPVEGSRYA<ADWRRYRRGYYGRRHGPPRDYAG<EEEEEGSGSSEGFD
ParentalPPATDRQFSGARNQLRRPQYRPQYRQRRFPPYHVGQTFDRRSRVLPHPNRIQAGEIGEMKDGVPEGAQLQ
PP.TDRQFSGARN.LRRPQYRPQYRQ.RFPPYHVGQTFDRRS.VLPHPNRIQA.EIGE.KDGVPEGAQLQ
RetrocopyPPTTDRQFSGARNRLRRPQYRPQYRQQRFPPYHVGQTFDRRSPVLPHPNRIQAVEIGELKDGVPEGAQLQ
ParentalGPVHRNPTYRPRYRSRGPPRPRPAPAVGEAEDKENQQATSGPNQPSVRRGYRRPYNYRRRPRPPNAPSQD
GP.HRNPTYRPRY.SRGPPRPRPAPAVGEAEDKENQQA.SGPNQP.VRRGYRRPYNYRRRPR.PNAPSQD
RetrocopyGPFHRNPTYRPRYHSRGPPRPRPAPAVGEAEDKENQQASSGPNQPPVRRGYRRPYNYRRRPRSPNAPSQD
ParentalGKEAKAGEAPTENPAPPTQQSSAE
GKEA.AGEAPTENPAP.T.QSSAE
RetrocopyGKEATAGEAPTENPAPSTEQSSAE

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 442 .46 RPM
bodymap2_adrenal 0 .00 RPM 238 .31 RPM
bodymap2_brain 0 .02 RPM 42 .03 RPM
bodymap2_breast 0 .00 RPM 253 .56 RPM
bodymap2_colon 0 .00 RPM 476 .92 RPM
bodymap2_heart 0 .07 RPM 406 .36 RPM
bodymap2_kidney 0 .19 RPM 152 .11 RPM
bodymap2_liver 0 .00 RPM 18 .14 RPM
bodymap2_lung 0 .00 RPM 679 .40 RPM
bodymap2_lymph_node 0 .00 RPM 252 .78 RPM
bodymap2_ovary 0 .00 RPM 207 .34 RPM
bodymap2_prostate 0 .05 RPM 380 .76 RPM
bodymap2_skeletal_muscle 1 .71 RPM 8342 .22 RPM
bodymap2_testis 3 .54 RPM 472 .40 RPM
bodymap2_thyroid 0 .04 RPM 720 .65 RPM
bodymap2_white_blood_cells 0 .00 RPM 79 .07 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1674 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1674 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_512931028 libraries686 libraries105 libraries9 libraries1 library
TSS #2 TSS_51294319 libraries442 libraries844 libraries175 libraries49 libraries

The graphical summary, for retro_hsap_1674 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_1674 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1674 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000060471 retrocopy
retro_hsap_637,
Homo sapiens ENSG00000060138 1 retrocopy
retro_hsap_1674 ,
Homo sapiens ENSG000000659784 retrocopies
retro_hsap_1433, retro_hsap_3886, retro_hsap_4250, retro_hsap_4301,
Pongo abelii ENSPPYG000000042791 retrocopy
retro_pabe_1420,
Tupaia belangeri ENSTBEG000000125701 retrocopy
retro_tbel_996,

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 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .18 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .15 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .09 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 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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