RetrogeneDB ID:

retro_hsap_2568

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:17075975..17076378(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000240122
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FABP5
Ensembl ID:ENSG00000164687
Aliases:FABP5, E-FABP, EFABP, KFABP, PA-FABP, PAFABP
Description:fatty acid binding protein 5 (psoriasis-associated) [Source:HGNC Symbol;Acc:3560]


Retrocopy-Parental alignment summary:






>retro_hsap_2568
ATGGCCACAGTTCAGCAGCTGGAAGGAAGATGGCGCCTGGTGGACAGCGAAGGCTTTGATGAATACATGAAGGAGCTAGG
AGGAAATAGCTTTGCAAAAAATGGGCGCAATGGCCAAGCCAGATTGTATCATCACTTGTGATGGCAAAAACCTCACCATA
AAAACTGAGAGCACTTTGAAAACAACACAGTTTTCTTGTACCCTGGGAGAGAAGTTTGAAGAAACCACAGCTGATGGCAG
AAAAACTCAGACTGTGTGCAACTTTACAGATGGTGCATTGGTTCAGCATCAGGAGTGGGATGGGAAGGAAAGCACAATAA
CAAGAACATTGAAAGATGGGAAATTAGTGGTGGACTGTGTCATGAACCATGTCGCCTGTACTCGGATCTATGAAAAAGTA
CAA

ORF - retro_hsap_2568 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.18 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMATVQQLEGRWRLVDSKGFDEYMKELGVGIALRK-MGAMAKPDCIITCDGKNLTIKTESTLKTTQFSCTL
MATVQQLEGRWRLVDS.GFDEYMKELG.G....K.MGAMAKPDCIITCDGKNLTIKTESTLKTTQFSCTL
RetrocopyMATVQQLEGRWRLVDSEGFDEYMKELG-GNSFAK>MGAMAKPDCIITCDGKNLTIKTESTLKTTQFSCTL
ParentalGEKFEETTADGRKTQTVCNFTDGALVQHQEWDGKESTITRKLKDGKLVVECVMNNVTCTRIYEKVE
GEKFEETTADGRKTQTVCNFTDGALVQHQEWDGKESTITR.LKDGKLVV.CVMN.V.CTRIYEKV.
RetrocopyGEKFEETTADGRKTQTVCNFTDGALVQHQEWDGKESTITRTLKDGKLVVDCVMNHVACTRIYEKVQ

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 19 .10 RPM
bodymap2_adrenal 0 .02 RPM 30 .15 RPM
bodymap2_brain 0 .00 RPM 20 .77 RPM
bodymap2_breast 0 .02 RPM 44 .65 RPM
bodymap2_colon 0 .00 RPM 21 .44 RPM
bodymap2_heart 0 .00 RPM 14 .62 RPM
bodymap2_kidney 0 .02 RPM 2 .48 RPM
bodymap2_liver 0 .00 RPM 0 .42 RPM
bodymap2_lung 0 .00 RPM 14 .24 RPM
bodymap2_lymph_node 0 .00 RPM 31 .58 RPM
bodymap2_ovary 0 .02 RPM 4 .59 RPM
bodymap2_prostate 0 .00 RPM 21 .62 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .60 RPM
bodymap2_testis 0 .00 RPM 11 .88 RPM
bodymap2_thyroid 0 .06 RPM 7 .38 RPM
bodymap2_white_blood_cells 0 .00 RPM 1 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2568 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2568 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_1063831339 libraries390 libraries97 libraries2 libraries1 library

The graphical summary, for retro_hsap_2568 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_2568 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2568 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1498
Parental genes homology:
Parental genes homology involve 29 parental genes, and 108 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000146191 retrocopy
retro_amel_1139,
Bos taurus ENSBTAG000000473303 retrocopies
retro_btau_1312, retro_btau_1828, retro_btau_886,
Callithrix jacchus ENSCJAG000000004444 retrocopies
retro_cjac_1832, retro_cjac_2227, retro_cjac_2816, retro_cjac_4084,
Cavia porcellus ENSCPOG000000257321 retrocopy
retro_cpor_948,
Dasypus novemcinctus ENSDNOG000000180665 retrocopies
retro_dnov_1073, retro_dnov_1231, retro_dnov_1318, retro_dnov_2392, retro_dnov_559,
Equus caballus ENSECAG000000082702 retrocopies
retro_ecab_894, retro_ecab_938,
Erinaceus europaeus ENSEEUG000000140232 retrocopies
retro_eeur_405, retro_eeur_627,
Echinops telfairi ENSETEG0000000744314 retrocopies
retro_etel_1024, retro_etel_1241, retro_etel_1276, retro_etel_1405, retro_etel_1467, retro_etel_1706, retro_etel_1842, retro_etel_1904, retro_etel_2003, retro_etel_512, retro_etel_602, retro_etel_620, retro_etel_806, retro_etel_994,
Felis catus ENSFCAG000000060322 retrocopies
retro_fcat_1243, retro_fcat_1834,
Homo sapiens ENSG000001217691 retrocopy
retro_hsap_1258,
Homo sapiens ENSG000001644341 retrocopy
retro_hsap_536,
Homo sapiens ENSG00000164687 12 retrocopies
retro_hsap_1205, retro_hsap_1279, retro_hsap_1520, retro_hsap_1521, retro_hsap_2167, retro_hsap_2568 , retro_hsap_3000, retro_hsap_3357, retro_hsap_3376, retro_hsap_3811, retro_hsap_4717, retro_hsap_880,
Homo sapiens ENSG000001974161 retrocopy
retro_hsap_3679,
Latimeria chalumnae ENSLACG000000085113 retrocopies
retro_lcha_37, retro_lcha_45, retro_lcha_57,
Macropus eugenii ENSMEUG000000021361 retrocopy
retro_meug_1874,
Microcebus murinus ENSMICG000000013112 retrocopies
retro_mmur_137, retro_mmur_702,
Myotis lucifugus ENSMLUG000000095143 retrocopies
retro_mluc_1590, retro_mluc_1920, retro_mluc_501,
Macaca mulatta ENSMMUG000000004864 retrocopies
retro_mmul_1417, retro_mmul_1920, retro_mmul_2095, retro_mmul_2230,
Mus musculus ENSMUSG000000275334 retrocopies
retro_mmus_1685, retro_mmus_1791, retro_mmus_2084, retro_mmus_3185,
Otolemur garnettii ENSOGAG0000000241310 retrocopies
retro_ogar_1024, retro_ogar_1151, retro_ogar_1286, retro_ogar_1676, retro_ogar_2873, retro_ogar_3066, retro_ogar_3099, retro_ogar_3265, retro_ogar_715, retro_ogar_878,
Oryzias latipes ENSORLG000000082821 retrocopy
retro_olat_7,
Pongo abelii ENSPPYG000000186991 retrocopy
retro_pabe_27,
Pan troglodytes ENSPTRG0000002037312 retrocopies
retro_ptro_1029, retro_ptro_1030, retro_ptro_1498, retro_ptro_1654, retro_ptro_2029, retro_ptro_2131, retro_ptro_2265, retro_ptro_2295, retro_ptro_2664, retro_ptro_3135, retro_ptro_823, retro_ptro_875,
Pteropus vampyrus ENSPVAG000000178505 retrocopies
retro_pvam_1159, retro_pvam_467, retro_pvam_531, retro_pvam_852, retro_pvam_89,
Rattus norvegicus ENSRNOG000000490753 retrocopies
retro_rnor_1762, retro_rnor_1879, retro_rnor_1997,
Sus scrofa ENSSSCG000000061531 retrocopy
retro_sscr_476,
Ictidomys tridecemlineatus ENSSTOG000000078773 retrocopies
retro_itri_1305, retro_itri_389, retro_itri_72,
Tarsius syrichta ENSTSYG000000014725 retrocopies
retro_tsyr_126, retro_tsyr_1534, retro_tsyr_1894, retro_tsyr_1982, retro_tsyr_2024,
Tursiops truncatus ENSTTRG000000053771 retrocopy
retro_ttru_1800,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 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 .03 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 .02 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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