RetrogeneDB ID:

retro_hsap_5

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:107037450..107037912(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000170935
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:NCBP2
Ensembl ID:ENSG00000114503
Aliases:NCBP2, CBC2, CBP20, NIP1
Description:nuclear cap binding protein subunit 2, 20kDa [Source:HGNC Symbol;Acc:7659]


Retrocopy-Parental alignment summary:






>retro_hsap_5
ATGTCCAAAGACCTGAAAATTCTATGTAAAGACCCTGCTTTGGAGCTGAGCTGCTACCGGGACCATCAGTTCAGTGGCCG
TAAATTTCAGCAGGAAAAATTACTGAAGGAAAGCTCCACATTGAATATGGGGAATCTTTCCTTTTATACAACCGAAGAGA
AAATACATGAACTCTTTAGTAGATCTGATATCAGGAATATCTTTATGGGCCTGGATAAAATAAAGAAAACAGCATGTGGT
TTTTGCTTTGTAGAATGCCATAACAGAGCTGATGCTGAAAATGCCATGCGGTTTCTAACTGGGACCTGCCTAGATGAATG
GATTATCTGCACTGATTGGGATGTCGGTTTTAGAGAGGGTCAACAGTATGGTCGCGGTAAATCTGGGGGTCAGGTAAGGG
ATGAGTTTCGTGAAGATTTTCATTCTGGTAGAGGAGGCTTTGGAAGACAGACTCAGATCTAG

ORF - retro_hsap_5 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.11 %
Parental protein coverage: 95.51 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK
LK.L..D...ELS.YRD..F.G....QEKLLK.S.TL..GNLSFYTTEE.I.ELFS.S.DI..I.MGLDK
RetrocopyLKILCKDPALELSCYRDHQFSGRKFQQEKLLKESSTLNMGNLSFYTTEEKIHELFSRS-DIRNIFMGLDK
ParentalMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAG
.KKTACGFCFVE...RADAENAMR...GT.LD..II.TDWD.GF.EG.QYGRG.SGGQVRDE.R.D...G
RetrocopyIKKTACGFCFVECHNRADAENAMRFLTGTCLDEWIICTDWDVGFREGQQYGRGKSGGQVRDEFREDFHSG
ParentalRGGYGKLAQ
RGG.G...Q
RetrocopyRGGFGRQTQ

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 .04 RPM 67 .31 RPM
bodymap2_adrenal 0 .10 RPM 99 .79 RPM
bodymap2_brain 0 .14 RPM 80 .09 RPM
bodymap2_breast 0 .06 RPM 78 .83 RPM
bodymap2_colon 0 .00 RPM 90 .76 RPM
bodymap2_heart 0 .00 RPM 38 .29 RPM
bodymap2_kidney 0 .08 RPM 84 .23 RPM
bodymap2_liver 0 .00 RPM 22 .01 RPM
bodymap2_lung 0 .11 RPM 46 .98 RPM
bodymap2_lymph_node 0 .00 RPM 78 .19 RPM
bodymap2_ovary 0 .66 RPM 108 .66 RPM
bodymap2_prostate 0 .03 RPM 83 .90 RPM
bodymap2_skeletal_muscle 0 .13 RPM 28 .25 RPM
bodymap2_testis 0 .81 RPM 89 .23 RPM
bodymap2_thyroid 0 .34 RPM 105 .87 RPM
bodymap2_white_blood_cells 0 .00 RPM 65 .05 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_5 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_5 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_5 retrocopy 5' end.

Lab - click to see more details

retro_hsap_5 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_5 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3151
Pongo abelii retro_pabe_85
Oryctolagus cuniculus retro_ocun_1887
Bos taurus retro_btau_1819
Canis familiaris retro_cfam_152
Equus caballus retro_ecab_79
Parental genes homology:
Parental genes homology involve 25 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000036642 retrocopies
retro_amel_113, retro_amel_62,
Bos taurus ENSBTAG000000088731 retrocopy
retro_btau_1819,
Canis familiaris ENSCAFG000000131002 retrocopies
retro_cfam_152, retro_cfam_2195,
Callithrix jacchus ENSCJAG000000137352 retrocopies
retro_cjac_3139, retro_cjac_4103,
Cavia porcellus ENSCPOG000000029761 retrocopy
retro_cpor_611,
Equus caballus ENSECAG000000161531 retrocopy
retro_ecab_79,
Felis catus ENSFCAG000000298652 retrocopies
retro_fcat_1936, retro_fcat_561,
Homo sapiens ENSG00000114503 1 retrocopy
retro_hsap_5 ,
Loxodonta africana ENSLAFG000000063721 retrocopy
retro_lafr_129,
Macropus eugenii ENSMEUG000000047301 retrocopy
retro_meug_34,
Microcebus murinus ENSMICG000000031621 retrocopy
retro_mmur_488,
Myotis lucifugus ENSMLUG000000175002 retrocopies
retro_mluc_355, retro_mluc_592,
Mustela putorius furoENSMPUG000000038061 retrocopy
retro_mputfur_9,
Mus musculus ENSMUSG000000227742 retrocopies
retro_mmus_2381, retro_mmus_2645,
Nomascus leucogenys ENSNLEG000000017271 retrocopy
retro_nleu_1239,
Oryctolagus cuniculus ENSOCUG000000067382 retrocopies
retro_ocun_1887, retro_ocun_833,
Otolemur garnettii ENSOGAG000000050096 retrocopies
retro_ogar_3151, retro_ogar_3152, retro_ogar_3153, retro_ogar_3160, retro_ogar_3161, retro_ogar_3162,
Pongo abelii ENSPPYG000000144491 retrocopy
retro_pabe_85,
Pan troglodytes ENSPTRG000000157891 retrocopy
retro_ptro_3151,
Pteropus vampyrus ENSPVAG000000172733 retrocopies
retro_pvam_238, retro_pvam_305, retro_pvam_939,
Sarcophilus harrisii ENSSHAG000000043632 retrocopies
retro_shar_161, retro_shar_46,
Tupaia belangeri ENSTBEG000000152223 retrocopies
retro_tbel_2153, retro_tbel_3367, retro_tbel_758,
Tarsius syrichta ENSTSYG000000142631 retrocopy
retro_tsyr_2008,
Tursiops truncatus ENSTTRG000000139082 retrocopies
retro_ttru_442, retro_ttru_826,
Vicugna pacos ENSVPAG000000103691 retrocopy
retro_vpac_493,

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 .02 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 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 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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