RetrogeneDB ID:

retro_hsap_553

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:30669227..30669994(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000214434
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MKI67IP
Ensembl ID:ENSG00000155438
Aliases:NIFK, MKI67IP, Nopp34
Description:MKI67 (FHA domain) interacting nucleolar phosphoprotein [Source:HGNC Symbol;Acc:17838]


Retrocopy-Parental alignment summary:






>retro_hsap_553
CAACTTTCTCCTGGTGTAGTCTATGTGCGCCACCTACCTAATCTACTTAAGGAAACCCAGATCCTTTCCTATTTCTCCCA
GTGTGACACTGTTACAAGGTTCAGACTGTCCAGAAAGAAAAGGACTGGAAATAGCAAAGGCTATGCATTTGTGGAGTTTG
AGTCTGAGGATGTTGCCAAGATAGTTACTGAAACAATGAACAGCTACCTATTTGGTGAAAGACTCTTGGAGTGTCATTTT
ATGCCACCTGAAAAAGTACAGAAATAACTCTTTTAAAGACTGGAATATTCCATTTAAGCAGCCGTCATATCCATCAGTGA
AACGGTATAATCAGAATCGGCACTTACACAAAAGCTACGGATGGAGGAGCGATTTAAAAAGGAAAGAAAGAAAGAAAGAT
TTCTCGGAAGAAATTAGCTTAAAAAGGAATTGACTATGATTTTCCTTCTTTGATTTTACAGAAAATGGAAAGCATTTCAA
AAACGAATCATCGGATGTCTACAAAAGGCCAGGTTTTACGTAAGAAGAAGAAAAAGGTTTTAGGCACTCCTGACACTCTT
GAAAAGACTGTGGATAGCCAGGGCCCCACACCGGTTTGTACATCAACATTTTTGGAGAGATGAAAATCTGAAGTGGCTGA
AATGAAGGATGATGATGAAGATAATGAAATAGTTTTCAAACAGCCCATATCCTGTGTAAAAGAAGAAATACAAGATACTC
AAACACCTACACATTCACAGAAAAAAAGACGAAGAAAAAGCAATCAG

ORF - retro_hsap_553 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.33 %
Parental protein coverage: 86.35 %
Number of stop codons detected: 3
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalQLTPGVVYVRHLPNLLDETQIFSYFSQFGTVTRFRLSRSKRTGNSKGYAFVEFESEDVAKIVAETMNNYL
QL.PGVVYVRHLPNLL.ETQI.SYFSQ..TVTRFRLSR.KRTGNSKGYAFVEFESEDVAKIV.ETMN.YL
RetrocopyQLSPGVVYVRHLPNLLKETQILSYFSQCDTVTRFRLSRKKRTGNSKGYAFVEFESEDVAKIVTETMNSYL
ParentalFGERLLECHFMPPEKVHKELF-KDWNIPFKQPSYPSVKRYNRNR-TLTQKLRMEERF---KKKERLL-RK
FGERLLECHFMPPEKV.K.LF.KDWNIPFKQPSYPSVKRYN.NR..LTQKLRMEERF....KKER.L.RK
RetrocopyFGERLLECHFMPPEKVQK*LF>KDWNIPFKQPSYPSVKRYNQNR<ALTQKLRMEERFKKERKKERFL<RK
ParentalKLAKKGIDYDFPSLILQKTESISKTNRQTSTKGQVLRKKKKKVSGTLDTPEKTVDSQGPTPVCTPTFLER
KLA.KGIDYDFPSLILQK.ESISKTN...STKGQVLRKKKKKV.GT.DT.EKTVDSQGPTPVCT.TFLER
RetrocopyKLA*KGIDYDFPSLILQKMESISKTNHRMSTKGQVLRKKKKKVLGTPDTLEKTVDSQGPTPVCTSTFLER
ParentalRKSQVAELNDDDKDDEIVFKQPISCVKEEIQETQTPTHSRKKRRRSSNQ
.KS.VAE..DDD.D.EIVFKQPISCVKEEIQ.TQTPTHS.KKRRR.SNQ
Retrocopy*KSEVAEMKDDDEDNEIVFKQPISCVKEEIQDTQTPTHSQKKRRRKSNQ

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 18 .01 RPM
bodymap2_adrenal 0 .00 RPM 37 .81 RPM
bodymap2_brain 0 .00 RPM 19 .13 RPM
bodymap2_breast 0 .00 RPM 15 .43 RPM
bodymap2_colon 0 .00 RPM 29 .53 RPM
bodymap2_heart 0 .00 RPM 9 .93 RPM
bodymap2_kidney 0 .00 RPM 30 .30 RPM
bodymap2_liver 0 .00 RPM 21 .04 RPM
bodymap2_lung 0 .00 RPM 19 .08 RPM
bodymap2_lymph_node 0 .00 RPM 24 .80 RPM
bodymap2_ovary 0 .00 RPM 47 .96 RPM
bodymap2_prostate 0 .00 RPM 31 .90 RPM
bodymap2_skeletal_muscle 0 .00 RPM 31 .32 RPM
bodymap2_testis 0 .00 RPM 34 .84 RPM
bodymap2_thyroid 0 .00 RPM 39 .43 RPM
bodymap2_white_blood_cells 0 .00 RPM 40 .95 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_553 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_553 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_553 retrocopy 5' end.

Lab - click to see more details

retro_hsap_553 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_553 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_415
Pongo abelii retro_pabe_510
Macaca mulatta retro_mmul_2389
Parental genes homology:
Parental genes homology involve 19 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000193871 retrocopy
retro_btau_1516,
Choloepus hoffmanni ENSCHOG000000022275 retrocopies
retro_chof_1061, retro_chof_1449, retro_chof_1735, retro_chof_236, retro_chof_2480,
Callithrix jacchus ENSCJAG000000133861 retrocopy
retro_cjac_3076,
Dasypus novemcinctus ENSDNOG000000050172 retrocopies
retro_dnov_1869, retro_dnov_2487,
Erinaceus europaeus ENSEEUG000000085353 retrocopies
retro_eeur_530, retro_eeur_550, retro_eeur_91,
Homo sapiens ENSG00000155438 5 retrocopies
retro_hsap_1077, retro_hsap_1596, retro_hsap_1609, retro_hsap_1611, retro_hsap_553 ,
Gorilla gorilla ENSGGOG000000234984 retrocopies
retro_ggor_1213, retro_ggor_1923, retro_ggor_2225, retro_ggor_850,
Loxodonta africana ENSLAFG000000307311 retrocopy
retro_lafr_500,
Microcebus murinus ENSMICG000000157871 retrocopy
retro_mmur_990,
Myotis lucifugus ENSMLUG000000064812 retrocopies
retro_mluc_1217, retro_mluc_1369,
Macaca mulatta ENSMMUG0000002092811 retrocopies
retro_mmul_1444, retro_mmul_1544, retro_mmul_2149, retro_mmul_2151, retro_mmul_2225, retro_mmul_2226, retro_mmul_2389, retro_mmul_690, retro_mmul_696, retro_mmul_697, retro_mmul_752,
Monodelphis domestica ENSMODG000000001522 retrocopies
retro_mdom_1271, retro_mdom_737,
Nomascus leucogenys ENSNLEG000000011634 retrocopies
retro_nleu_1756, retro_nleu_1942, retro_nleu_2022, retro_nleu_669,
Pongo abelii ENSPPYG000000258752 retrocopies
retro_pabe_2248, retro_pabe_510,
Pan troglodytes ENSPTRG000000124195 retrocopies
retro_ptro_1072, retro_ptro_1077, retro_ptro_1080, retro_ptro_1378, retro_ptro_415,
Pteropus vampyrus ENSPVAG000000167071 retrocopy
retro_pvam_134,
Sorex araneus ENSSARG000000062521 retrocopy
retro_sara_362,
Tupaia belangeri ENSTBEG000000011234 retrocopies
retro_tbel_1731, retro_tbel_3479, retro_tbel_4589, retro_tbel_926,
Vicugna pacos ENSVPAG000000058472 retrocopies
retro_vpac_136, retro_vpac_265,

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 .03 RPM
GBR_HG00111 0 .02 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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