RetrogeneDB ID:

retro_hsap_3839

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:37625105..37625932(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000178503
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NECAP1
Ensembl ID:ENSG00000089818
Aliases:None
Description:NECAP endocytosis associated 1 [Source:HGNC Symbol;Acc:24539]


Retrocopy-Parental alignment summary:






>retro_hsap_3839
ATGGTGGCCAAGTTGGAGTATGAGTCTGTGCTGTGTGTGAAGCCAAACATCAGCGTCTACTGGATTCCTCCCTGGGCCTC
CAACTGTGATTACAGGGCATCTGACTGGAAATTAGACCAGCCTGATTGGACTGTTCACCTCCGAATCATTTCAAAAGGGA
AGACTGCCTATATCAAACTCGAGGATAAAGTTTCAGGGGAGCTCTTCACTCAGATACCAGTAGAACAATATCCTGGTATT
GCTGTGGAGACAGTGACAGATTCCAGCTGCTACTTTTTAATCTGGATTCAGGATGGTCCTGGGCAGAGTGCTGTCATTGA
CACTGCTGGCTTCACAGATCGGGGAGATGCCTTTGAATTTAATGTCTCCTTGCAGGATCACTTCAAATGGGTAAAGCAGG
AATCTGAGATTTCCAAGGAATCTCAAGAAATGGACGCTTGTCCTAACTTGGATCTGGGCTTCAAAGAAAGACAAACCATC
AAGTTGAGTACGGGGAACATTACAACCAAGAATGGATGTGCTTCTAAGCCCAGGACTGCAATGGGTGGGGGCCTGAGCTT
ACTCGCATCCCCACCAGGAGGCCAAGTCAGTATTCCCCCACTGTCCTCCTCAGTTGCATCAGCAATCATGTCACCCTACC
AGCCATTCCAAAATCTAACCATGGAGGCAGTGATGCAGATATCCTTTTAGATTTGGATTCTCCTGCTCCTGTCACAACAC
CAGCACCAACTCCAGTTTCTGCAAGCAATGACTTGTGGGGAGACTTCAGCACTGCATCCAGCTCTGTTCCAAACCAGGCA
CCACAGCCATCCAACTGGGTCCAATTC

ORF - retro_hsap_3839 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.84 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMATELEYESVLCVKPDVSVYRIPPRASNRGYRASDWKLDQPDWTGRLRITSKGKTAYIKLEDKVSGELFA
M...LEYESVLCVKP..SVY.IPP.ASN..YRASDWKLDQPDWT..LRI.SKGKTAYIKLEDKVSGELF.
RetrocopyMVAKLEYESVLCVKPNISVYWIPPWASNCDYRASDWKLDQPDWTVHLRIISKGKTAYIKLEDKVSGELFT
ParentalQAPVEQYPGIAVETVTDSSRYFVIRIQDGTGRSAFIG-IGFTDRGDAFDFNVSLQDHFKWVKQESEISKE
Q.PVEQYPGIAVETVTDSS.YF.I.IQDG.G.SA.I...GFTDRGDAF.FNVSLQDHFKWVKQESEISKE
RetrocopyQIPVEQYPGIAVETVTDSSCYFLIWIQDGPGQSAVIDTAGFTDRGDAFEFNVSLQDHFKWVKQESEISKE
ParentalSQEMDARPKLDLGFKEGQTIKLCIGNITNKKGGASKPRTARGGGLSLLPPPPGGKVTIPPPSSSVA-ISN
SQEMDA.P.LDLGFKE.QTIKL..GNIT.K.G.ASKPRTA.GGGLSLL..PPGG.V.IPP.SSSVA.ISN
RetrocopySQEMDACPNLDLGFKERQTIKLSTGNITTKNGCASKPRTAMGGGLSLLASPPGGQVSIPPLSSSVA<ISN
ParentalHVTPPPIPKSNHGGSDADILLDLDSPAPVTTPAPTPVSVSNDLWGDFSTASSSVPNQAPQPSNWVQF
HVT.P.IPKSNHGGSDADILLDLDSPAPVTTPAPTPVS.SNDLWGDFSTASSSVPNQAPQPSNWVQF
RetrocopyHVTLPAIPKSNHGGSDADILLDLDSPAPVTTPAPTPVSASNDLWGDFSTASSSVPNQAPQPSNWVQF

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 .08 RPM
bodymap2_adrenal 0 .00 RPM 32 .06 RPM
bodymap2_brain 0 .00 RPM 124 .14 RPM
bodymap2_breast 0 .00 RPM 20 .14 RPM
bodymap2_colon 0 .00 RPM 23 .01 RPM
bodymap2_heart 0 .00 RPM 14 .90 RPM
bodymap2_kidney 0 .00 RPM 36 .40 RPM
bodymap2_liver 0 .00 RPM 20 .07 RPM
bodymap2_lung 0 .00 RPM 25 .07 RPM
bodymap2_lymph_node 0 .00 RPM 39 .76 RPM
bodymap2_ovary 0 .00 RPM 38 .44 RPM
bodymap2_prostate 0 .00 RPM 46 .28 RPM
bodymap2_skeletal_muscle 0 .00 RPM 12 .37 RPM
bodymap2_testis 0 .00 RPM 35 .24 RPM
bodymap2_thyroid 0 .00 RPM 32 .13 RPM
bodymap2_white_blood_cells 0 .00 RPM 42 .62 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3839 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3839 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3839 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3839 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3839 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2615
Pongo abelii retro_pabe_3059
Parental genes homology:
Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000169891 retrocopy
retro_amel_1016,
Canis familiaris ENSCAFG000000139301 retrocopy
retro_cfam_780,
Choloepus hoffmanni ENSCHOG000000080873 retrocopies
retro_chof_1692, retro_chof_1818, retro_chof_1913,
Dasypus novemcinctus ENSDNOG000000147782 retrocopies
retro_dnov_613, retro_dnov_986,
Homo sapiens ENSG00000089818 1 retrocopy
retro_hsap_3839 ,
Gorilla gorilla ENSGGOG000000102331 retrocopy
retro_ggor_2585,
Loxodonta africana ENSLAFG000000029791 retrocopy
retro_lafr_632,
Mustela putorius furoENSMPUG000000167421 retrocopy
retro_mputfur_361,
Nomascus leucogenys ENSNLEG000000017431 retrocopy
retro_nleu_1974,
Otolemur garnettii ENSOGAG000000063581 retrocopy
retro_ogar_3442,
Pongo abelii ENSPPYG000000042381 retrocopy
retro_pabe_3059,
Pan troglodytes ENSPTRG000000232771 retrocopy
retro_ptro_2615,
Rattus norvegicus ENSRNOG000000092361 retrocopy
retro_rnor_1806,
Ictidomys tridecemlineatus ENSSTOG000000101532 retrocopies
retro_itri_1107, retro_itri_740,
Tursiops truncatus ENSTTRG000000142601 retrocopy
retro_ttru_1035,

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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