RetrogeneDB ID:

retro_hsap_3679

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:149625220..149625588(-)
Located in intron of:ENSG00000055208
Retrocopy
information
Ensembl ID:ENSG00000216265
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FABP12
Ensembl ID:ENSG00000197416
Aliases:None
Description:fatty acid binding protein 12 [Source:HGNC Symbol;Acc:34524]


Retrocopy-Parental alignment summary:






>retro_hsap_3679
AGTTCACAGACTTTTGTTACTGAAGGAATAGGGAGAGCCAGCAGGAAACTGGCTGCCTGGCAAAACCCATGGTGACCATC
AGTAGAAATGGAGATGTGATCACTATAAAAATGAAAAGCATCTTTAAAAATAATGAGATTGCTTTTAAACCTAGAAAAGT
GTGAGGAAACCACACCAGGTGGCCATAAAATCAAGAGTACCATAACCTTAGATAATGACTCCCTGATTCAGGTTCAGGAC
TGGGATCACAAGGAGACCTCATTGGGAGAAAGTTGGTGGGTGAGAAGATGGGGGTGGAAAGTGCCGTGAGCAATATTACC
TGTGCTCAGATATAGGGGAGAGAATGAACAAATTCAGTCTCAAACTCC

ORF - retro_hsap_3679 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.81 %
Parental protein coverage: 89.29 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalNSEDYMKELGIGRASRKL-GRLAKPTVTISTDGDVITI-KTKSIFKNNEISFKLGEEFEEITPGGHKTKS
.S.....E.GIGRASRKL.G.LAKP.VTIS..GDVITI.K.K...K.......L.E..EE.TPGGHK.KS
RetrocopySSQTFVTE-GIGRASRKL<GCLAKPMVTISRNGDVITI>K*KASLKIMRLLLNL-EKCEETTPGGHKIKS
ParentalKVTLDKESLIQVQDWDGKETT-ITRKLVDGKMVVESTVNSVICTRTYEKVSSNSVSNS
..TLD..SLIQVQDWD.KET..I.RKLV..KM.VES.V....C.........NSVSNS
RetrocopyTITLDNDSLIQVQDWDHKETS<IGRKLVGEKMGVESAVSNITCAQI*GRE*TNSVSNS

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 0 .06 RPM
bodymap2_adrenal 0 .00 RPM 0 .00 RPM
bodymap2_brain 0 .00 RPM 0 .00 RPM
bodymap2_breast 0 .00 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .00 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 1 .60 RPM
bodymap2_thyroid 0 .00 RPM 0 .08 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3679 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3679 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3679 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3679 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3679 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2493
Gorilla gorilla retro_ggor_2488
Pongo abelii retro_pabe_3016
Macaca mulatta retro_mmul_1787
Callithrix jacchus retro_cjac_2486
Equus caballus retro_ecab_761
Parental genes homology:
Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000145541 retrocopy
retro_amel_945,
Callithrix jacchus ENSCJAG000000004331 retrocopy
retro_cjac_2486,
Equus caballus ENSECAG000000235521 retrocopy
retro_ecab_761,
Homo sapiens ENSG000001217691 retrocopy
retro_hsap_1258,
Homo sapiens ENSG000001644341 retrocopy
retro_hsap_536,
Homo sapiens ENSG0000016468712 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 ENSG00000197416 1 retrocopy
retro_hsap_3679 ,
Gorilla gorilla ENSGGOG000000168351 retrocopy
retro_ggor_2488,
Latimeria chalumnae ENSLACG000000085113 retrocopies
retro_lcha_37, retro_lcha_45, retro_lcha_57,
Microcebus murinus ENSMICG000000053191 retrocopy
retro_mmur_1131,
Macaca mulatta ENSMMUG000000193371 retrocopy
retro_mmul_1787,
Nomascus leucogenys ENSNLEG000000025151 retrocopy
retro_nleu_528,
Oryzias latipes ENSORLG000000082821 retrocopy
retro_olat_7,
Pongo abelii ENSPPYG000000187031 retrocopy
retro_pabe_3016,
Pan troglodytes ENSPTRG000000226541 retrocopy
retro_ptro_2493,

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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