RetrogeneDB ID:

retro_hsap_4047

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:39855387..39855849(-)
Located in intron of:ENSG00000188676
Retrocopy
information
Ensembl ID:ENSG00000253790
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NFYB
Ensembl ID:ENSG00000120837
Aliases:NFYB, CBF-A, CBF-B, HAP3, NF-YB
Description:nuclear transcription factor Y, beta [Source:HGNC Symbol;Acc:7805]


Retrocopy-Parental alignment summary:






>retro_hsap_4047
TCAAAAGAAAGTTGCAGAGAACAAAATATACATTTTCTGATTGCACATGTCACTAGGATAATGAAACATGCCATATCTCA
AATGGGAAATGCCCAAGAAAGTGTTAAACAACGTGTACGTGTGTTCATCAGCTTTATAACACCTGAGGCAAGTGAAAGAT
GCCCCCAAGAGAAACAGAAATGGCCAGTGGAGAGGATTTTCACTTTGCCATGTCTACCATAGGCTTTGACAGTTATATGG
AACCTCTGAAATTATCCCTCAGAAACTCAGAAAGGCTGTGAAAGGAGAGAAGGGAATTGGTGGAGAAGTCAGAGCTACAG
ATGGGCTAAGTGAGGAGCTTACAGAATAGGCATTTGCTAGCCAGTCACCAGCCGGCTTCATACCTGCTGCTGGGCAGCAA
CAAATGTTATGACTTATGTACCACCATAGCAAGAGATTTCTGGTGTTCAACAAATTCTGTTT

ORF - retro_hsap_4047 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.43 %
Parental protein coverage: 76.81 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSKESFREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRK-TINGE
SKES.REQ.I...IA.V.RIMK.AI.Q.G.....A.E.V...V..FISFIT.EASERC.QEK.K....GE
RetrocopySKESCREQNIHFLIAHVTRIMKHAISQMG----NAQESVKQRVRVFISFITPEASERCPQEKQK<MASGE
ParentalDILFAMSTLGFDSYVEPLKLYL-QKFREAMKGEKGIGGAVTATDGLSEELTEEAFTNQLPAGLITTDGQQ
D..FAMST.GFDSY.EPLKL.L.QK.R.A.KGEKGIGG.V.ATDGLSEELTE.AF..Q.PAG.I...GQQ
RetrocopyDFHFAMSTIGFDSYMEPLKLSL<QKLRKAVKGEKGIGGEVRATDGLSEELTE*AFASQSPAGFIPAAGQQ
ParentalQ-NVMVYTTSYQQISGVQQIQF
Q.NVM.Y....Q.ISGVQQI.F
RetrocopyQ<NVMTYVPP*QEISGVQQILF

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 33 .08 RPM
bodymap2_adrenal 0 .00 RPM 45 .83 RPM
bodymap2_brain 0 .00 RPM 60 .41 RPM
bodymap2_breast 0 .00 RPM 39 .44 RPM
bodymap2_colon 0 .00 RPM 99 .12 RPM
bodymap2_heart 0 .00 RPM 42 .76 RPM
bodymap2_kidney 0 .15 RPM 49 .90 RPM
bodymap2_liver 0 .00 RPM 14 .77 RPM
bodymap2_lung 0 .00 RPM 50 .55 RPM
bodymap2_lymph_node 0 .00 RPM 76 .48 RPM
bodymap2_ovary 0 .00 RPM 70 .19 RPM
bodymap2_prostate 0 .00 RPM 81 .23 RPM
bodymap2_skeletal_muscle 0 .00 RPM 28 .57 RPM
bodymap2_testis 0 .00 RPM 84 .78 RPM
bodymap2_thyroid 0 .00 RPM 48 .57 RPM
bodymap2_white_blood_cells 0 .00 RPM 31 .19 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4047 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4047 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4047 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4047 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4047 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066861 retrocopy
retro_amel_940,
Bos taurus ENSBTAG000000307441 retrocopy
retro_btau_1681,
Canis familiaris ENSCAFG000000291771 retrocopy
retro_cfam_1677,
Callithrix jacchus ENSCJAG000000146101 retrocopy
retro_cjac_1133,
Cavia porcellus ENSCPOG000000032131 retrocopy
retro_cpor_901,
Felis catus ENSFCAG000000264711 retrocopy
retro_fcat_207,
Homo sapiens ENSG00000120837 2 retrocopies
retro_hsap_2827, retro_hsap_4047 ,
Gorilla gorilla ENSGGOG000000088661 retrocopy
retro_ggor_2714,
Myotis lucifugus ENSMLUG000000054681 retrocopy
retro_mluc_1764,
Macaca mulatta ENSMMUG000000225703 retrocopies
retro_mmul_1433, retro_mmul_2119, retro_mmul_2335,
Mustela putorius furoENSMPUG000000120643 retrocopies
retro_mputfur_1531, retro_mputfur_1563, retro_mputfur_1567,
Nomascus leucogenys ENSNLEG000000065432 retrocopies
retro_nleu_1203, retro_nleu_2061,
Oryctolagus cuniculus ENSOCUG000000044154 retrocopies
retro_ocun_1334, retro_ocun_1816, retro_ocun_1824, retro_ocun_1845,
Ochotona princeps ENSOPRG000000081172 retrocopies
retro_opri_36, retro_opri_657,
Ictidomys tridecemlineatus ENSSTOG000000052791 retrocopy
retro_itri_1851,
Tupaia belangeri ENSTBEG000000057311 retrocopy
retro_tbel_4360,

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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