RetrogeneDB ID:

retro_hsap_4150

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:33624259..33625288(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000231991
Aliases:ANXA2P2, ANX2L2, ANX2P2, LPC2B
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ANXA2
Ensembl ID:ENSG00000182718
Aliases:ANXA2, ANX2, ANX2L4, CAL1H, HEL-S-270, LIP2, LPC2, LPC2D, P36, PAP-IV
Description:annexin A2 [Source:HGNC Symbol;Acc:537]


Retrocopy-Parental alignment summary:






>retro_hsap_4150
GCTTCCTTCAAAATGTCTACTGTTCACGAAATCCTGTGCAAGCTCAGCTTGGAGGGTGATCACTCTACACCCCCAAGTGC
ATATGGGTCTGTCAAAGCCTACACTAACTTTGATGCTGAGCGGGATGCTTTGAACATTGAAACAGCCATCAAGACCAAAG
GTGTGGATGAGGTCACCATTGTCAACATTGTGACCAACCGCGACAATGCACAGAGACAGGATATTGTCTTCTCCTACCAG
AGAAGGACCAAAAAGGAACTTGCATCAGCACTGAAGTCAGCCTTATCTGGCCACCTGGAGACGGTGATTTTGGGCCTATT
GAAGACACCTGCTCAGTATGACGCTTCTGAGCTAAAAGCTTCCATGAAGGGGCTAGGAACCGACGAGGACTCTCTCATTG
AGATCATCTGCTCCAGAACCAACCAGGAGCTGCAGGAAATTAACAGAGTCTACAAGGAAATGTACAAGACTGATCTGGAG
AAGGACATTATTTCGGACACATCTGGTGACTTCCGCAAGCTGATGGTTGCCCTGGCAAAGGGTAGAAGAGCAGAGGATGG
CTCTGTCATTGATTATGAACTGATTGACCAAGATGCCCAGGATCTCTATGACGCTGGAGTGAAGAGGAAAGGAACTGATG
TTCCCAAGTGGATCAGCATCATGACCGAGCGGAGCGTGCCCCACCTCCAGAAAGTATTTGATAGGTACAAGAGTTACAGC
CCTTATGACATGTTGGAAAGCATCAGGAAAGAGGTTAAAGGAGACCTGGAAAATGCTTTCCTGAACCTGGTCCAGCGCAT
TCAGAACAAGCCCTTGTATTTTGCTGATCAGCTGTACGACTCCATGAAGGGCAAGGGGACGCGAGATAAGGTCCTGATCA
GAATCATGGTCTCCCGCAGTGAAGTGGACATGTTGAAAATTAGGTCTGAATTCAAGAGAAAGTACGGCAAGTCCCTGTAC
TATTACATCCAGCAAGACACTAAGGGCGACTACCAGAAAGCGCTGCTGTACCTGTGTGGTGGAGACGAC

ORF - retro_hsap_4150 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.96 %
Parental protein coverage: 96.08 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalASFKMSTVHEILCKLSLEGDHSTPPSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNA
ASFKMSTVHEILCKLSLEGDHSTPPSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNI.TNR.NA
RetrocopyASFKMSTVHEILCKLSLEGDHSTPPSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNIVTNRDNA
ParentalQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRT
QRQDI.F.YQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRT
RetrocopyQRQDIVFSYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRT
ParentalNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRK
NQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDA.DLYDAGVKRK
RetrocopyNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDAQDLYDAGVKRK
ParentalGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYD
GTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQ.IQNKPLYFAD.LYD
RetrocopyGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQRIQNKPLYFADQLYD
ParentalSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD
SMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD
RetrocopySMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD

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 1 .71 RPM 424 .91 RPM
bodymap2_adrenal 2 .11 RPM 421 .08 RPM
bodymap2_brain 0 .28 RPM 38 .49 RPM
bodymap2_breast 5 .91 RPM 922 .91 RPM
bodymap2_colon 1 .10 RPM 271 .30 RPM
bodymap2_heart 0 .09 RPM 87 .08 RPM
bodymap2_kidney 3 .89 RPM 287 .25 RPM
bodymap2_liver 0 .19 RPM 43 .87 RPM
bodymap2_lung 1 .35 RPM 629 .22 RPM
bodymap2_lymph_node 3 .38 RPM 239 .73 RPM
bodymap2_ovary 1 .31 RPM 201 .83 RPM
bodymap2_prostate 2 .51 RPM 259 .37 RPM
bodymap2_skeletal_muscle 0 .55 RPM 102 .14 RPM
bodymap2_testis 1 .13 RPM 242 .68 RPM
bodymap2_thyroid 1 .47 RPM 260 .62 RPM
bodymap2_white_blood_cells 3 .37 RPM 369 .26 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4150 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4150 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_19268742 libraries20 libraries133 libraries135 libraries1499 libraries
TSS #2 TSS_192688188 libraries185 libraries509 libraries314 libraries633 libraries
TSS #3 TSS_192690976 libraries587 libraries255 libraries10 libraries1 library

The graphical summary, for retro_hsap_4150 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_4150 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4150 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_81
Parental genes homology:
Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000166863 retrocopies
retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Homo sapiens ENSG00000182718 3 retrocopies
retro_hsap_3114, retro_hsap_4150 , retro_hsap_580,
Gorilla gorilla ENSGGOG000000097383 retrocopies
retro_ggor_2137, retro_ggor_2788, retro_ggor_515,
Macropus eugenii ENSMEUG000000089803 retrocopies
retro_meug_1000, retro_meug_312, retro_meug_389,
Myotis lucifugus ENSMLUG000000024643 retrocopies
retro_mluc_1569, retro_mluc_2223, retro_mluc_2431,
Monodelphis domestica ENSMODG000000116041 retrocopy
retro_mdom_1471,
Mustela putorius furoENSMPUG000000007622 retrocopies
retro_mputfur_73, retro_mputfur_79,
Nomascus leucogenys ENSNLEG000000116782 retrocopies
retro_nleu_769, retro_nleu_802,
Pongo abelii ENSPPYG000000065262 retrocopies
retro_pabe_2572, retro_pabe_607,
Pan troglodytes ENSPTRG000000071322 retrocopies
retro_ptro_2106, retro_ptro_81,

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 = 0.94 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .28 RPM
CEU_NA11843 0 .28 RPM
CEU_NA11930 0 .55 RPM
CEU_NA12004 0 .19 RPM
CEU_NA12400 0 .35 RPM
CEU_NA12751 0 .12 RPM
CEU_NA12760 0 .76 RPM
CEU_NA12827 0 .33 RPM
CEU_NA12872 0 .19 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .30 RPM
FIN_HG00277 0 .41 RPM
FIN_HG00315 0 .55 RPM
FIN_HG00321 0 .33 RPM
FIN_HG00328 0 .24 RPM
FIN_HG00338 0 .23 RPM
FIN_HG00349 0 .48 RPM
FIN_HG00375 0 .56 RPM
FIN_HG00377 0 .40 RPM
FIN_HG00378 0 .32 RPM
GBR_HG00099 0 .61 RPM
GBR_HG00111 0 .32 RPM
GBR_HG00114 0 .24 RPM
GBR_HG00119 0 .19 RPM
GBR_HG00131 0 .20 RPM
GBR_HG00133 0 .24 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .33 RPM
GBR_HG00142 0 .22 RPM
GBR_HG00143 0 .32 RPM
TSI_NA20512 0 .40 RPM
TSI_NA20513 0 .24 RPM
TSI_NA20518 0 .94 RPM
TSI_NA20532 0 .27 RPM
TSI_NA20538 0 .41 RPM
TSI_NA20756 0 .61 RPM
TSI_NA20765 0 .23 RPM
TSI_NA20771 0 .43 RPM
TSI_NA20786 0 .37 RPM
TSI_NA20798 0 .31 RPM
YRI_NA18870 0 .88 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .23 RPM
YRI_NA19093 0 .18 RPM
YRI_NA19099 0 .69 RPM
YRI_NA19114 0 .37 RPM
YRI_NA19118 0 .29 RPM
YRI_NA19213 0 .17 RPM
YRI_NA19214 0 .30 RPM
YRI_NA19223 0 .16 RPM

Indel association:

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





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