RetrogeneDB ID:

retro_hsap_4180

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:79585237..79585532(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236604
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LYPLA2
Ensembl ID:ENSG00000011009
Aliases:LYPLA2, APT-2, DJ886K2.4
Description:lysophospholipase II [Source:HGNC Symbol;Acc:6738]


Retrocopy-Parental alignment summary:






>retro_hsap_4180
CACAGCTGGGCTGAGCCCTGTCCACCATCCGGCTCCCTCATGTCAAGTACATCCATATCTGTCCCCTTGTGCCTAGGATC
CCTGTGACACTGAACATGAAGACGGTGATGCCCTCCTAGTTTGACCCAATGGGGCTGAGTCCAGGTGCCTCAGAGGACGA
GGCTGGCATCAAGAAGGCAGTAGAGAACTTAAGGTCCCAGCCTCTCCTCGGCCTCCTCCCTTCCCTGTCCCCCCAGGAAA
GCACTGGGCAGTGCCCCTGTCTGGCTCCCTTCCTGGGCCCCTTGGCAGCTTCCCC

ORF - retro_hsap_4180 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.05 %
Parental protein coverage: 72.26 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalHSWAD-ALSTIRLPHVKYI--CPHAPRIPVTLNMKMVMPSWFDLMGLSPDAPEDEAGIKKAAENRRG-PV
HSWA..ALSTIRLPHVKYI..CP..PRIPVTLNMK.VMPS.FD.MGLSP.A.EDEAGIKKA.EN.R..P.
RetrocopyHSWAE<ALSTIRLPHVKYIHICPLVPRIPVTLNMKTVMPS*FDPMGLSPGASEDEAGIKKAVENLRS<PA
ParentalPLHGPHLPPPSGWHRGVELLAASAPGLPPGECP
....P..P.P.G.H..V..L..S.PG.P.G..P
RetrocopySPRPPPFPVPPGKHWAVP-LSGSLPG-PLGSFP

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 23 .56 RPM
bodymap2_adrenal 0 .00 RPM 24 .97 RPM
bodymap2_brain 0 .00 RPM 6 .94 RPM
bodymap2_breast 0 .00 RPM 12 .28 RPM
bodymap2_colon 0 .00 RPM 17 .44 RPM
bodymap2_heart 0 .00 RPM 8 .20 RPM
bodymap2_kidney 0 .00 RPM 39 .89 RPM
bodymap2_liver 0 .00 RPM 26 .97 RPM
bodymap2_lung 0 .00 RPM 20 .41 RPM
bodymap2_lymph_node 0 .00 RPM 26 .02 RPM
bodymap2_ovary 0 .00 RPM 15 .25 RPM
bodymap2_prostate 0 .00 RPM 17 .32 RPM
bodymap2_skeletal_muscle 0 .00 RPM 14 .26 RPM
bodymap2_testis 0 .00 RPM 16 .14 RPM
bodymap2_thyroid 0 .00 RPM 19 .90 RPM
bodymap2_white_blood_cells 0 .00 RPM 34 .20 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_4180 was not detected
No EST(s) were mapped for retro_hsap_4180 retrocopy.
No TSS is located nearby retro_hsap_4180 retrocopy 5' end.
retro_hsap_4180 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4180 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000116251 retrocopy
Callithrix jacchus ENSCJAG000000209141 retrocopy
Dasypus novemcinctus ENSDNOG000000112852 retrocopies
Homo sapiens ENSG00000011009 3 retrocopies
retro_hsap_2023, retro_hsap_3577, retro_hsap_4180 ,
Homo sapiens ENSG000001209923 retrocopies
Macropus eugenii ENSMEUG000000047682 retrocopies
Nomascus leucogenys ENSNLEG000000086461 retrocopy
Otolemur garnettii ENSOGAG000000322601 retrocopy

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 ) 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 .00 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 .00 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 .00 RPM
YRI_NA19214 0 .00 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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