RetrogeneDB ID:

retro_hsap_1701

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:72038138..72038474(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000263311
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CCDC25
Ensembl ID:ENSG00000147419
Aliases:None
Description:coiled-coil domain containing 25 [Source:HGNC Symbol;Acc:25591]


Retrocopy-Parental alignment summary:






>retro_hsap_1701
CATGAAGATCTGATGAAGCATGGCTGGCCTGAATATATCTGGTTTCGTGCGGACAGACTCTCTTTGGCTCATGTATACCT
TCAATTGCATAAGGGAGAGAATATAGAGGACATTCCAAAGGAAGTGCTGACAGACTGCGCCCACCTTGTGAAGGCCAATA
GCACTCAAGGCTGCAAGAACAACGTTAATGTGGTAAATACTCCACGGTCTAACCTGAAGAAAACAGCTGACGTGGATGTG
AGGCAGATAGGCTTTCACAGGCAGAAGGATGTAAAAATTGTGACAATGGAGAAGAAAGTAAATGAGATCCTGAACCGATT
AGAAAAAACCAAAGTG

ORF - retro_hsap_1701 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.84 %
Parental protein coverage: 54.33 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNEDLIKHGWPEDIWFHVDKLSSAHVYLRLHKGENIEDIPKEVLMDCAHLVKANSIQGCKMNNVNVVYTPW
.EDL.KHGWPE.IWF..D.LS.AHVYL.LHKGENIEDIPKEVL.DCAHLVKANS.QGCK.NNVNVV.TP.
RetrocopyHEDLMKHGWPEYIWFRADRLSLAHVYLQLHKGENIEDIPKEVLTDCAHLVKANSTQGCK-NNVNVVNTPR
ParentalSNLKKTADMDVGQIGFHRQKDVKIVTVEKKVNEILNRLEKTKV
SNLKKTAD.DV.QIGFHRQKDVKIVT.EKKVNEILNRLEKTKV
RetrocopySNLKKTADVDVRQIGFHRQKDVKIVTMEKKVNEILNRLEKTKV

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 55 .88 RPM
bodymap2_adrenal 0 .20 RPM 68 .41 RPM
bodymap2_brain 0 .00 RPM 82 .11 RPM
bodymap2_breast 0 .00 RPM 54 .11 RPM
bodymap2_colon 0 .00 RPM 41 .44 RPM
bodymap2_heart 0 .02 RPM 35 .35 RPM
bodymap2_kidney 0 .00 RPM 45 .99 RPM
bodymap2_liver 0 .17 RPM 44 .51 RPM
bodymap2_lung 0 .00 RPM 19 .60 RPM
bodymap2_lymph_node 0 .15 RPM 28 .91 RPM
bodymap2_ovary 0 .00 RPM 42 .14 RPM
bodymap2_prostate 0 .00 RPM 45 .97 RPM
bodymap2_skeletal_muscle 0 .00 RPM 39 .52 RPM
bodymap2_testis 0 .04 RPM 58 .29 RPM
bodymap2_thyroid 0 .00 RPM 98 .32 RPM
bodymap2_white_blood_cells 0 .00 RPM 37 .76 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1701 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1701 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1701 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1701 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1701 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1274
Pongo abelii retro_pabe_1364
Parental genes homology:
Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000129712 retrocopies
retro_chof_2254, retro_chof_847,
Dipodomys ordii ENSDORG000000065951 retrocopy
retro_dord_491,
Echinops telfairi ENSETEG000000064781 retrocopy
retro_etel_434,
Homo sapiens ENSG00000147419 1 retrocopy
retro_hsap_1701 ,
Gorilla gorilla ENSGGOG000000096851 retrocopy
retro_ggor_1274,
Monodelphis domestica ENSMODG000000159761 retrocopy
retro_mdom_511,
Pongo abelii ENSPPYG000000184682 retrocopies
retro_pabe_1364, retro_pabe_477,
Pan troglodytes ENSPTRG000000201091 retrocopy
retro_ptro_141,
Tarsius syrichta ENSTSYG000000007321 retrocopy
retro_tsyr_1364,

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 .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 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 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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