RetrogeneDB ID:

retro_hsap_3485

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:71874778..71875470(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000218350
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LYPLA1
Ensembl ID:ENSG00000120992
Aliases:LYPLA1, APT-1, APT1, LPL-I, LPL1, hAPT1
Description:lysophospholipase I [Source:HGNC Symbol;Acc:6737]


Retrocopy-Parental alignment summary:






>retro_hsap_3485
ATGTGCGGCAATAACATGTCAACCCCGCTGCCCACCATCGTGCCCGCCCCCCGGAAGGCCACCACTGAGGTGATTTTCCT
GCATGGATTGGGAGATACTGGGCACGGATGGGCAGAAGCCTTTGCCGGTATCATAAGTTCACATATCAAATATATCTGCC
CGCATGCGCCTGTTAGGCCTGTTAACATTAAATATGAACATAGCTATGCCTTCATGGTTTGATATTATTGGGCTTTCACC
AGATTCACAGGAGGATGAATCTGGGATTAAACAGGCAGCACAAAATATAAAAGCTTTGATTGATCAAGAAGTGAAGAATG
GCATTCCTTCTAACAGAATTATTTTGGGAGGGTTTTCTCAGGGAGGAGCTTTATCTTTATATACTGCCCTTACCACGCAC
CAGAAACTGGCAGGTGTCACTGCACTCAATTGCTGGCTTCCACTTTGGGCTTCCTTTCCACAGGGTCCTATCGGTGGTGC
TAATAGAGATATTTCTATTCTCCAGTGCCACGGGGATTGTGACCCTTTGGTTCCCCTGATGTTTGGTTCTCTTACGGTTG
AAAAACTAAAAAACATTGGTGAATCCAGCCAATGTGACCTTTAAAACCTATGAAGGTATGATGCACAGTTCGTGTCAACA
GGAAATGATGAATGTCAAGCAATTCATTGATAAACTCCTACCTCCAATTGAT

ORF - retro_hsap_3485 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.4 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMCGNNMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPV-TLNMNVAM
MCGNNMSTPLP.IVPA.RKAT..VIFLHGLGDTGHGWAEAFAGI.SSHIKYICPHAPVRPV.TLNMN.AM
RetrocopyMCGNNMSTPLPTIVPAPRKATTEVIFLHGLGDTGHGWAEAFAGIISSHIKYICPHAPVRPV>TLNMNIAM
ParentalPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGV
PSWFDIIGLSPDSQEDESGIKQAA.NIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTT.QKLAGV
RetrocopyPSWFDIIGLSPDSQEDESGIKQAAQNIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTHQKLAGV
ParentalTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLK-TLVNPANVTFKTYEGMMH
TAL.CWLPL.ASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLK.TLVNPANVTFKTYEGMMH
RetrocopyTALNCWLPLWASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLK>TLVNPANVTFKTYEGMMH
ParentalSSCQQEMMDVKQFIDKLLPPID
SSCQQEMM.VKQFIDKLLPPID
RetrocopySSCQQEMMNVKQFIDKLLPPID

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 40 .79 RPM
bodymap2_adrenal 0 .00 RPM 46 .61 RPM
bodymap2_brain 0 .09 RPM 16 .88 RPM
bodymap2_breast 0 .10 RPM 50 .97 RPM
bodymap2_colon 0 .00 RPM 44 .38 RPM
bodymap2_heart 0 .02 RPM 68 .12 RPM
bodymap2_kidney 0 .17 RPM 110 .52 RPM
bodymap2_liver 0 .00 RPM 66 .54 RPM
bodymap2_lung 0 .02 RPM 48 .10 RPM
bodymap2_lymph_node 0 .00 RPM 54 .00 RPM
bodymap2_ovary 0 .15 RPM 33 .73 RPM
bodymap2_prostate 0 .00 RPM 66 .56 RPM
bodymap2_skeletal_muscle 0 .02 RPM 44 .81 RPM
bodymap2_testis 0 .06 RPM 116 .87 RPM
bodymap2_thyroid 0 .02 RPM 46 .31 RPM
bodymap2_white_blood_cells 0 .02 RPM 102 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3485 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3485 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_167471984 libraries172 libraries495 libraries135 libraries43 libraries
TSS #2 TSS_1674721378 libraries300 libraries147 libraries4 libraries0 libraries

The graphical summary, for retro_hsap_3485 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_3485 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3485 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000069781 retrocopy
retro_cfam_523,
Callithrix jacchus ENSCJAG000000115622 retrocopies
retro_cjac_1260, retro_cjac_3100,
Cavia porcellus ENSCPOG000000227153 retrocopies
retro_cpor_142, retro_cpor_549, retro_cpor_782,
Dipodomys ordii ENSDORG000000014791 retrocopy
retro_dord_88,
Equus caballus ENSECAG000000165301 retrocopy
retro_ecab_238,
Echinops telfairi ENSETEG000000017272 retrocopies
retro_etel_612, retro_etel_791,
Homo sapiens ENSG000000110093 retrocopies
retro_hsap_2023, retro_hsap_3577, retro_hsap_4180,
Homo sapiens ENSG00000120992 3 retrocopies
retro_hsap_3078, retro_hsap_3485 , retro_hsap_3897,
Myotis lucifugus ENSMLUG000000082081 retrocopy
retro_mluc_1683,
Macaca mulatta ENSMMUG000000131573 retrocopies
retro_mmul_1734, retro_mmul_2459, retro_mmul_2474,
Nomascus leucogenys ENSNLEG000000010274 retrocopies
retro_nleu_1137, retro_nleu_2015, retro_nleu_2817, retro_nleu_2869,
Oryctolagus cuniculus ENSOCUG000000067513 retrocopies
retro_ocun_1510, retro_ocun_1623, retro_ocun_1679,
Pteropus vampyrus ENSPVAG000000052462 retrocopies
retro_pvam_224, retro_pvam_838,
Rattus norvegicus ENSRNOG000000083203 retrocopies
retro_rnor_1747, retro_rnor_2612, retro_rnor_406,
Tarsius syrichta ENSTSYG000000123506 retrocopies
retro_tsyr_1287, retro_tsyr_1303, retro_tsyr_1465, retro_tsyr_1901, retro_tsyr_1996, retro_tsyr_2158,
Tursiops truncatus ENSTTRG000000118363 retrocopies
retro_ttru_1643, retro_ttru_169, retro_ttru_291,

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 = 0.28 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 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 .07 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .28 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .07 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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