RetrogeneDB ID:

retro_hsap_3713

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:29251916..29252499(+)
Located in intron of:ENSG00000106069
Retrocopy
information
Ensembl ID:ENSG00000237065
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NANOG
Ensembl ID:ENSG00000111704
Aliases:None
Description:Nanog homeobox [Source:HGNC Symbol;Acc:20857]


Retrocopy-Parental alignment summary:






>retro_hsap_3713
ATGAGTGTGGATCTGGCTTGTCTGCAAAGCTTGCCTTGCTTCGAAGCATCCGACTGTAAAGAATCTTAACCTATGGCTGT
GATTTGTGGGCCTGAAGAAAACTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACGGAGACTGTCTCTCCTC
TTCTTCCTCCATGGATCTGCTTATTCAGGACAGCCCTGATTCTTCCACCAGTCCCAAAGGCAAACAACCCATTGCTGCAG
AGAATAATGCCCCAAAAAAGGGAGACGAGGTCCCAGTCAAGAAACAGAAGACCAGAACTGTGTTTTCTTCCACCCAGCTG
TGTGTACTCAATGATAGATTTCAGAGACAGAAATACCTTAGCCTCCAGCAGATGCAAGAACTCTCCAATATCTGGAACCT
CAGCTACAAACAGGTGAAGACCTGGTTCTAGAACCAGAGAATGAAATCTAAGAGGTGGCAGAAAAACAACTGGCCGAAGA
ATAGCAATGGTGTGACTCGGAAGGCCTCAGCACCTACCTACCCCAGCCACTACTCTTCCTACCACCAGGGATGACTGGTG
ACCTGACTGGGAACCTTCCAATG

ORF - retro_hsap_3713 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.83 %
Parental protein coverage: 63.93 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSVDPACPQSLPCFEASDCKESSPMPVICGPEENYPSLQMSSAEMPHTETVSPL-PSSMDLLIQDSPDSS
MSVD.AC.QSLPCFEASDCKES.PM.VICGPEENYPSLQMSSAEMPHTETVSPL..SSMDLLIQDSPDSS
RetrocopyMSVDLACLQSLPCFEASDCKES*PMAVICGPEENYPSLQMSSAEMPHTETVSPL<SSSMDLLIQDSPDSS
ParentalTSPKGKQPTSAEKSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV
TSPKGKQP..AE....KK.D.VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNI.NLSYKQV
RetrocopyTSPKGKQPIAAENNAPKKGDEVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNIWNLSYKQV
ParentalKTWFQNQRMKSKRWQKNNWPKNSNGVTQKASAPTYPSLYSSYHQGCLV-NPTGNLPM
KTWF.NQRMKSKRWQKNNWPKNSNGVT.KASAPTYPS.YSSYHQG.LV...TGNLPM
RetrocopyKTWF*NQRMKSKRWQKNNWPKNSNGVTRKASAPTYPSHYSSYHQG*LV<DLTGNLPM

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 .00 RPM
bodymap2_adrenal 0 .00 RPM 0 .00 RPM
bodymap2_brain 0 .00 RPM 0 .02 RPM
bodymap2_breast 0 .00 RPM 0 .00 RPM
bodymap2_colon 0 .29 RPM 0 .10 RPM
bodymap2_heart 0 .09 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .30 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 .02 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 0 .13 RPM
bodymap2_thyroid 0 .00 RPM 0 .00 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_3713 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3713 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3713 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3713 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3713 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2514
Gorilla gorilla retro_ggor_2510
Pongo abelii retro_pabe_3142
Parental genes homology:
Parental genes homology involve 22 parental genes, and 59 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000170641 retrocopy
retro_amel_354,
Canis familiaris ENSCAFG000000139141 retrocopy
retro_cfam_724,
Choloepus hoffmanni ENSCHOG000000009724 retrocopies
retro_chof_1267, retro_chof_264, retro_chof_794, retro_chof_987,
Cavia porcellus ENSCPOG000000026211 retrocopy
retro_cpor_1132,
Echinops telfairi ENSETEG000000046488 retrocopies
retro_etel_1155, retro_etel_1334, retro_etel_134, retro_etel_1434, retro_etel_1935, retro_etel_630, retro_etel_818, retro_etel_963,
Felis catus ENSFCAG000000016211 retrocopy
retro_fcat_932,
Homo sapiens ENSG00000111704 5 retrocopies
retro_hsap_1455, retro_hsap_1549, retro_hsap_3713 , retro_hsap_4814, retro_hsap_722,
Gorilla gorilla ENSGGOG000000281964 retrocopies
retro_ggor_1812, retro_ggor_2510, retro_ggor_3000, retro_ggor_608,
Macropus eugenii ENSMEUG000000099492 retrocopies
retro_meug_266, retro_meug_940,
Microcebus murinus ENSMICG000000022281 retrocopy
retro_mmur_575,
Myotis lucifugus ENSMLUG000000293252 retrocopies
retro_mluc_1562, retro_mluc_2054,
Myotis lucifugus ENSMLUG000000305801 retrocopy
retro_mluc_169,
Macaca mulatta ENSMMUG000000321584 retrocopies
retro_mmul_1901, retro_mmul_2466, retro_mmul_964, retro_mmul_979,
Monodelphis domestica ENSMODG000000179792 retrocopies
retro_mdom_1293, retro_mdom_1938,
Mustela putorius furoENSMPUG000000167315 retrocopies
retro_mputfur_1140, retro_mputfur_1553, retro_mputfur_261, retro_mputfur_553, retro_mputfur_691,
Nomascus leucogenys ENSNLEG000000053593 retrocopies
retro_nleu_1086, retro_nleu_2189, retro_nleu_2340,
Oryctolagus cuniculus ENSOCUG000000137831 retrocopy
retro_ocun_971,
Otolemur garnettii ENSOGAG000000263391 retrocopy
retro_ogar_568,
Procavia capensis ENSPCAG000000154602 retrocopies
retro_pcap_143, retro_pcap_429,
Pongo abelii ENSPPYG000000042335 retrocopies
retro_pabe_2157, retro_pabe_3142, retro_pabe_3440, retro_pabe_3742, retro_pabe_623,
Pan troglodytes ENSPTRG000000298074 retrocopies
retro_ptro_1746, retro_ptro_2514, retro_ptro_3203, retro_ptro_990,
Pteropus vampyrus ENSPVAG000000069891 retrocopy
retro_pvam_1251,

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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