RetrogeneDB ID:

retro_hsap_4280

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:89699075..89700066(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000224887
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NFYC
Ensembl ID:ENSG00000066136
Aliases:NFYC, CBF-C, CBFC, H1TF2A, HAP5, HSM, NF-YC
Description:nuclear transcription factor Y, gamma [Source:HGNC Symbol;Acc:7806]


Retrocopy-Parental alignment summary:






>retro_hsap_4280
ATGTCCACAGAAGGAGGATTTGGTGGTACTAGCCGCAGTGATGCCCAGCAAAGCCTAAAGTCCTTCTGGCTTCGGGTCAT
GGAAGAAATCTGGAATTTAGCAGTGAAAGATTTCTGAATGCAGGAACTCCCACTGGCTCGTATTAAGAAGATTATGAAAC
TGGATGAAGATGTGAAGATGATCAGTGCAGAGGCCCCTGTGCTCTTTGCCAGGGCAGCCCAGATTTTTTATCACAGAGTT
GACTCTTCGAGCCTGGATTCACACAGAGGATAACAACTGCCGGACTTATGTCGCCATGGCAATTACGAAATTTGATCAAT
TGGATTTTCTCATCGATATTGTTCTAAGAGATGAACTGAAACCTCCAAAGTGTCAGGAGGAGGTGCTGCAGTCTGTAACT
CCTGCTGAGCCAGTCCAATACTATTTCACGCTGGCTCAGCAGCCCACCGCCCGTCCAAGTCCAGGGACAGCAGCAAGGCC
AGACCACCGCCAGCTCCATGACCACCATGCAGCCTGGGCAGATCATCATCGCACAGCTTCAGCAGGGCCAGACCACGCCC
GTGACGACGCAGGTTGGAGAAGGTCAGCAGGTGCAGATTGTCCAGGCCCAGCCACAGGGTCAAGCCCAGTAGGCCCAGAG
TGGTACTGGATGGACCGTGCAGGTGATGTAGCAGATCCTCACTAACACAGGAGAGATCCAGCAGATCCCGGTGCAGCTGA
AGGCTGGCCAGCTGCAGTGTATCCGCTTAGCCCAGTCTGTATCAGGCACCCACGTTCTGCAGGGACAGATCCAGACACTT
GCCACCAGCGCTCAACCGATTACACAGACAGAGGTCCAGCAAAGACAGCAGTAGTTCAGCCAGTTCACAGATGGACAGCA
GCTCTACCAGATCCAGCAAGTATCCATACCTGCGGGCCAGGACCTGCCCAGCCCATGTTTTTCCAGTCAGTCAACCAGCC
CTCTGATGGGCAGGCCCCCCGGGTGACTGGC

ORF - retro_hsap_4280 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.76 %
Parental protein coverage: 99.7 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFA
MSTEGGFGGTS.SDAQQSL.SFW.RVMEEI.NL.VKDF..QELPLARIKKIMKLDEDVKMISAEAPVLFA
RetrocopyMSTEGGFGGTSRSDAQQSLKSFWLRVMEEIWNLAVKDF*MQELPLARIKKIMKLDEDVKMISAEAPVLFA
ParentalKAAQIF-ITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPA
.AAQIF.ITELTLRAWIHTEDN..RT......AMAITKFDQ.DFLIDIV.RDELKPPK.QEEV.QSVTPA
RetrocopyRAAQIF>ITELTLRAWIHTEDNNCRTY----VAMAITKFDQLDFLIDIVLRDELKPPKCQEEVLQSVTPA
ParentalEPVQYYFTLAQQPTA-VQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQP
EPVQYYFTLAQQPTA.VQVQGQQQGQ.T.SS.TT.QPGQIIIAQ.QQGQTTPVT.QVGEGQQVQIVQAQP
RetrocopyEPVQYYFTLAQQPTA>VQVQGQQQGQTTASSMTTMQPGQIIIAQLQQGQTTPVTTQVGEGQQVQIVQAQP
ParentalQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQIT
QGQAQ.AQSGTG.T.QVM.QI.TNTGEIQQIPVQL.AGQLQ.IRLAQ.VSGT.V.QGQIQTLAT.AQ.IT
RetrocopyQGQAQ*AQSGTGWTVQVM*QILTNTGEIQQIPVQLKAGQLQCIRLAQSVSGTHVLQGQIQTLATSAQPIT
ParentalQTEVQQGQQQFSQFTDGQQLYQIQQVTMPAGQDL-AQPMFIQSANQPSDGQAPQVTG
QTEVQQ.QQ.FSQFTDGQQLYQIQQV..PAGQDL.AQPMF.QS.NQPSDGQAP.VTG
RetrocopyQTEVQQRQQ*FSQFTDGQQLYQIQQVSIPAGQDL<AQPMFFQSVNQPSDGQAPRVTG

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 31 .29 RPM
bodymap2_adrenal 0 .00 RPM 49 .00 RPM
bodymap2_brain 0 .00 RPM 23 .63 RPM
bodymap2_breast 0 .00 RPM 32 .02 RPM
bodymap2_colon 0 .00 RPM 28 .19 RPM
bodymap2_heart 0 .00 RPM 28 .39 RPM
bodymap2_kidney 0 .00 RPM 40 .43 RPM
bodymap2_liver 0 .00 RPM 22 .12 RPM
bodymap2_lung 0 .00 RPM 23 .08 RPM
bodymap2_lymph_node 0 .00 RPM 40 .02 RPM
bodymap2_ovary 0 .00 RPM 44 .61 RPM
bodymap2_prostate 0 .00 RPM 52 .50 RPM
bodymap2_skeletal_muscle 0 .00 RPM 57 .38 RPM
bodymap2_testis 0 .26 RPM 43 .29 RPM
bodymap2_thyroid 0 .00 RPM 49 .53 RPM
bodymap2_white_blood_cells 0 .00 RPM 54 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4280 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4280 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4280 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4280 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4280 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2903
Gorilla gorilla retro_ggor_2865
Pongo abelii retro_pabe_3490
Macaca mulatta retro_mmul_1202
Parental genes homology:
Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000125911 retrocopy
retro_acar_33,
Bos taurus ENSBTAG000000219431 retrocopy
retro_btau_1338,
Callithrix jacchus ENSCJAG000000029871 retrocopy
retro_cjac_4050,
Homo sapiens ENSG00000066136 2 retrocopies
retro_hsap_4280 , retro_hsap_4668,
Homo sapiens ENSG000001153501 retrocopy
retro_hsap_2765,
Gorilla gorilla ENSGGOG000000073602 retrocopies
retro_ggor_2865, retro_ggor_2896,
Macropus eugenii ENSMEUG000000044801 retrocopy
retro_meug_1145,
Macaca mulatta ENSMMUG000000149702 retrocopies
retro_mmul_1202, retro_mmul_2485,
Mus musculus ENSMUSG000000328971 retrocopy
retro_mmus_844,
Otolemur garnettii ENSOGAG000000126142 retrocopies
retro_ogar_2147, retro_ogar_411,
Pongo abelii ENSPPYG000000014833 retrocopies
retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,
Pan troglodytes ENSPTRG000000005962 retrocopies
retro_ptro_2903, retro_ptro_3102,

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 = 0.03 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 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 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 .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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