RetrogeneDB ID:

retro_hsap_1329

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:42211864..42212166(+)
Located in intron of:ENSG00000165379
Retrocopy
information
Ensembl ID:ENSG00000258536
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FKBP1B
Ensembl ID:ENSG00000119782
Aliases:FKBP1B, FKBP12.6, FKBP1L, OTK4, PKBP1L, PPIase
Description:FK506 binding protein 1B, 12.6 kDa [Source:HGNC Symbol;Acc:3712]


Retrocopy-Parental alignment summary:






>retro_hsap_1329
GGGTCAAGAAGGACATTCACCAACAAGAGCCAGAAGAGCCAGGTGTGTGTAGCGCACTACATAGGGGTGTTCCAAAATGG
GAATAAATTTGATTTATCCGAAGACAGAAACAAACCTTTCAAGTTCAAAACTGGTGAACAGGAAGTCATCAGTGGTTTTG
AAGAGTACATAGCGCAGATGAGCTTGGGGCAGAAGGTGAAGCTGACCTGCATATGTGATGTGTCATATAGAGCTCCAGGC
TACTCTAGTATCATCCCTCCCAGTGCTATCCTATCTTTGACATGGAATTGCTCAACTTAGAG

ORF - retro_hsap_1329 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.73 %
Parental protein coverage: 90.74 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGDGRTFP---KKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTC
G..RTF.....K.Q.CV.HY.G..QNG.KFD.S.DRNKPFKF..G.QEVI.GFEE..AQMSLGQ..KLTC
RetrocopyGSRRTFTNKSQKSQVCVAHYIGVFQNGNKFDLSEDRNKPFKFKTGEQEVISGFEEYIAQMSLGQKVKLTC
ParentalTPDVAYGATGHPGVIPPNATL-IFDVELLNLE
..DV.Y.A.G....IPP.A.L.IFD.ELLNLE
RetrocopyICDVSYRAPGYSSIIPPSAIL<IFDMELLNLE

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 2 .23 RPM
bodymap2_adrenal 0 .00 RPM 1 .35 RPM
bodymap2_brain 0 .00 RPM 9 .68 RPM
bodymap2_breast 0 .00 RPM 0 .68 RPM
bodymap2_colon 0 .00 RPM 2 .32 RPM
bodymap2_heart 0 .00 RPM 0 .59 RPM
bodymap2_kidney 0 .00 RPM 3 .25 RPM
bodymap2_liver 0 .00 RPM 1 .25 RPM
bodymap2_lung 0 .00 RPM 4 .92 RPM
bodymap2_lymph_node 0 .00 RPM 2 .39 RPM
bodymap2_ovary 0 .00 RPM 2 .06 RPM
bodymap2_prostate 0 .16 RPM 2 .94 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .55 RPM
bodymap2_testis 0 .00 RPM 2 .09 RPM
bodymap2_thyroid 0 .00 RPM 2 .24 RPM
bodymap2_white_blood_cells 0 .00 RPM 2 .38 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1329 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1329 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1329 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1329 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1329 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_906
Gorilla gorilla retro_ggor_1036
Pongo abelii retro_pabe_1105
Macaca mulatta retro_mmul_2171
Callithrix jacchus retro_cjac_696
Parental genes homology:
Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000027971 retrocopy
retro_amel_1717,
Callithrix jacchus ENSCJAG000000077001 retrocopy
retro_cjac_696,
Ciona savignyi ENSCSAVG000000068591 retrocopy
retro_csav_11,
Equus caballus ENSECAG000000156641 retrocopy
retro_ecab_752,
Erinaceus europaeus ENSEEUG000000139202 retrocopies
retro_eeur_135, retro_eeur_514,
Echinops telfairi ENSETEG000000189902 retrocopies
retro_etel_186, retro_etel_2071,
Homo sapiens ENSG000000044785 retrocopies
retro_hsap_3085, retro_hsap_4162, retro_hsap_4165, retro_hsap_4264, retro_hsap_4266,
Homo sapiens ENSG000000888321 retrocopy
retro_hsap_1198,
Homo sapiens ENSG000000960604 retrocopies
retro_hsap_4255, retro_hsap_4260, retro_hsap_4262, retro_hsap_4318,
Homo sapiens ENSG00000119782 1 retrocopy
retro_hsap_1329 ,
Macropus eugenii ENSMEUG000000106891 retrocopy
retro_meug_14,
Microcebus murinus ENSMICG000000015301 retrocopy
retro_mmur_257,
Macaca mulatta ENSMMUG000000123411 retrocopy
retro_mmul_2171,
Nomascus leucogenys ENSNLEG000000008001 retrocopy
retro_nleu_1406,
Pongo abelii ENSPPYG000000126041 retrocopy
retro_pabe_1105,
Pan troglodytes ENSPTRG000000117081 retrocopy
retro_ptro_906,
Sorex araneus ENSSARG000000138081 retrocopy
retro_sara_24,
Tupaia belangeri ENSTBEG000000122821 retrocopy
retro_tbel_56,

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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