RetrogeneDB ID:

retro_hsap_3900

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:127497902..127498524(-)
Located in intron of:ENSG00000197157
Retrocopy
information
Ensembl ID:ENSG00000240579
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CD2BP2
Ensembl ID:ENSG00000169217
Aliases:CD2BP2, FWP010, LIN1, PPP1R59, Snu40, U5-52K
Description:CD2 (cytoplasmic tail) binding protein 2 [Source:HGNC Symbol;Acc:1656]


Retrocopy-Parental alignment summary:






>retro_hsap_3900
CGCCAGGCCTCAGACTTGGAAGAGGAGGACAGCTTGGGCCAGACCCCAGTGAGTGCCCAAGCCTTCTTGGAGGGACTTTT
GGAGCTCCTATTGCCTAGAGAGACAGTGGCTAGGGCACTGAGGCATCTGGGGGCCCGAGGAGGAGGCAAAGGGAGCAGCA
AGGGGCCTGGGTGACCCAGTTCCCCGCAGTGCCCGGACCGGCTCTCCGAATTGGCCGACCAGATGGTGGCCCAGGGAAAC
CTTGGCATGTACCAGGAAACGAGGGAACAGTTGGCCATGCGGCTGAAGGGTTTGGGGTGCCAGGCCCTAGGGACCCCACA
ATCCCACACCCCCACACTCCCTAGACATGTTCGCTGAGGAAGTGGCAGAGGGGGAACTGGAGACCCCAACCCCTACCCAG
AGAGGAGAAGCAGAGTTGCCAGGAGATGGTCTGGTGGATGTGATGTGGGAATATAAGTGGGAGAACCCGGGGGATGCCGA
GCTGCATGGGCCCTTCACCAGCGACCAGATGCAGACCTGGGTGAGCGAAGGCTACTTTCCTGATGGTGTTTACTGCCGGA
AGCTGGACCCCCTTCGTGGTCAGTTCTACAACTCCAAACGCATTGACTTTGACCTCTACACC

ORF - retro_hsap_3900 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.69 %
Parental protein coverage: 60.41 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRQASDSEEEDSLGQTSMSAQALLEGLLELLLPRETVAGALRRLGARGGGKGR-KGPGQPSSPQRLDRLSG
RQASD.EEEDSLGQT..SAQA.LEGLLELLLPRETVA.ALR.LGARGGGKG..KGPG.PSSPQ..DRLS.
RetrocopyRQASDLEEEDSLGQTPVSAQAFLEGLLELLLPRETVARALRHLGARGGGKGSSKGPG*PSSPQCPDRLSE
ParentalLADQMVARGNLGVYQETRERLAMRLKGLGCQTL-GPHNPTPPPSLDMFAEELAEEELETPTPTQRGEAES
LADQMVA.GNLG.YQETRE.LAMRLKGLGCQ.L.G..........DMFAEE.AE.ELETPTPTQRGEAE.
RetrocopyLADQMVAQGNLGMYQETREQLAMRLKGLGCQAL>GXXXXXXXXXXDMFAEEVAEGELETPTPTQRGEAEL
ParentalRGDGLVDVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT
.GDGLVDVMWEYKWEN.GDAEL.GPFTS.QMQTWVSEGYFPDGVYCRKLDP..GQFYNSKRIDFDLYT
RetrocopyPGDGLVDVMWEYKWENPGDAELHGPFTSDQMQTWVSEGYFPDGVYCRKLDPLRGQFYNSKRIDFDLYT

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 38 .58 RPM
bodymap2_adrenal 0 .12 RPM 51 .64 RPM
bodymap2_brain 0 .00 RPM 35 .51 RPM
bodymap2_breast 0 .00 RPM 36 .36 RPM
bodymap2_colon 0 .00 RPM 49 .85 RPM
bodymap2_heart 0 .00 RPM 19 .01 RPM
bodymap2_kidney 0 .00 RPM 43 .51 RPM
bodymap2_liver 0 .00 RPM 8 .60 RPM
bodymap2_lung 0 .09 RPM 40 .79 RPM
bodymap2_lymph_node 0 .00 RPM 56 .21 RPM
bodymap2_ovary 0 .12 RPM 58 .39 RPM
bodymap2_prostate 0 .00 RPM 59 .11 RPM
bodymap2_skeletal_muscle 0 .00 RPM 21 .26 RPM
bodymap2_testis 0 .00 RPM 46 .49 RPM
bodymap2_thyroid 0 .09 RPM 66 .85 RPM
bodymap2_white_blood_cells 0 .00 RPM 54 .52 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3900 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3900 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3900 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3900 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3900 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2653
Gorilla gorilla retro_ggor_2627
Pongo abelii retro_pabe_3179
Macaca mulatta retro_mmul_1735
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000169217 1 retrocopy
retro_hsap_3900 ,
Gorilla gorilla ENSGGOG000000142711 retrocopy
retro_ggor_2627,
Macaca mulatta ENSMMUG000000218441 retrocopy
retro_mmul_1735,
Nomascus leucogenys ENSNLEG000000157671 retrocopy
retro_nleu_1139,
Pongo abelii ENSPPYG000000072671 retrocopy
retro_pabe_3179,
Pan troglodytes ENSPTRG000000079951 retrocopy
retro_ptro_2653,

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 = 0.13 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .13 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 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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