RetrogeneDB ID:

retro_hsap_1624

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:11336538..11337406(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000263179
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPC
Ensembl ID:ENSG00000092199
Aliases:HNRNPC, C1, C2, HNRNP, HNRPC, SNRPC
Description:heterogeneous nuclear ribonucleoprotein C (C1/C2) [Source:HGNC Symbol;Acc:5035]


Retrocopy-Parental alignment summary:






>retro_hsap_1624
TCGCTCCATGAACGCGTGTTCGTTGGGAATCTCAACACTCTTGTGGTCAAGAAATCTGATGTGGAGGCAATCTTTTAGAA
GTATGGCAAAATTGTGGGCTGCGCTGTTCTTAAGGGCTTTGTTTTCATTCAGTATGTTAATGAGAGAAATGCCCGGGCCG
CTGTAGCAGCAGCAGATGGCAGAATAATCGCTGGCCAGGTTTTACATAGTAACCTGGCTGCAGAGCCAAAAGTGAACCGA
GGAAAAGCAGGTATGAAATGATCAGCAGTGGAGACGTACGGGTCAGAAACAGAACACCCTTCTCCATTCCTCTACTCAGC
TCCTCTTTTGACTTGGACTATGACTTTCAACGGGATTATGATAGGATGTACAGTTACCCAGCACGTGTACCTCCTCCTCC
TCCTATTGCTCGGGCTGTAGTGCCCTTGAAACATCAGCGTGTATCAGGAAACACCTCACAAAGGGGCAAAAGTGGCTTCA
ATTCTAAGAGTGGACAGCGGGGATCTTCCAAGTCTGGAAAGTTGAAAGGAGATGACCTTCAGGCCATTAAGCAGGAGTTG
ACCCAGATAAAACAAAAAGTGGATTCTCTCCTGGAAGACCCGGAAAAAATGGAAAAGAAACAGAGCAAACAAGCAGTAGA
GATGAAGAATGGTAAGTCAGAAGAGAAGCAGAGCAGCAGCTCACGTGAGACTCATGTGAAGATAGAGTCTGAAGGTGGTG
CAGATGACTCTGCTGAGGAGAGGGACCTACTGGATGATGAGGATAATGAAGATTGGGGGATGACCAGCTGGAGTTGATCA
AGGATGATGAAAAAGAGGCTGAGGAAGGAGAGGATGACAGAGACAGCACCAATGGTGAAGATGACTCT

ORF - retro_hsap_1624 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.47 %
Parental protein coverage: 96.08 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI
S...RVF.GNLNTLVVKKSDVEAIF.KYGKIVGC.V.KGF.F.QYVNERNARAAVA..DGR.IAGQVL..
RetrocopySLHERVFVGNLNTLVVKKSDVEAIF*KYGKIVGCAVLKGFVFIQYVNERNARAAVAAADGRIIAGQVLHS
ParentalNLAAEPKVNRGKAGVKRSAAEMYGSVTEHPSP-SPLLSSSFDLDYDFQRDYYDRMYSYPARVPPPPPIAR
NLAAEPKVNRGKAG.K.SA.E.YGS.TEHPSP..PLLSSSFDLDYDFQRD.YDRMYSYPARVPPPPPIAR
RetrocopyNLAAEPKVNRGKAGMK*SAVETYGSETEHPSP<IPLLSSSFDLDYDFQRD-YDRMYSYPARVPPPPPIAR
ParentalAVVPSKRQRVSGNTSRRGKSGFNSKSGQRGSSKSGKLKGDDLQAIKKELTQIKQKVDSLLENLEKIEKEQ
AVVP.K.QRVSGNTS.RGKSGFNSKSGQRGSSKSGKLKGDDLQAIK.ELTQIKQKVDSLLE..EK.EK.Q
RetrocopyAVVPLKHQRVSGNTSQRGKSGFNSKSGQRGSSKSGKLKGDDLQAIKQELTQIKQKVDSLLEDPEKMEKKQ
ParentalSKQAVEMKNDKSEEEQSSSSVKKDETNVKMESEGGADDSAEEGDLLDDDDNED-RGDDQLELIKDDEKEA
SKQAVEMKN.KSEE.QSSSS....ET.VK.ESEGGADDSAEE.DLLDD.DNED..GDDQLELIKDDEKEA
RetrocopySKQAVEMKNGKSEEKQSSSS---RETHVKIESEGGADDSAEERDLLDDEDNED<LGDDQLELIKDDEKEA
ParentalEEGEDDRDSANGEDDS
EEGEDDRDS.NGEDDS
RetrocopyEEGEDDRDSTNGEDDS

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 252 .87 RPM
bodymap2_adrenal 0 .27 RPM 354 .06 RPM
bodymap2_brain 0 .00 RPM 268 .86 RPM
bodymap2_breast 0 .06 RPM 217 .61 RPM
bodymap2_colon 0 .00 RPM 440 .95 RPM
bodymap2_heart 0 .00 RPM 106 .54 RPM
bodymap2_kidney 0 .06 RPM 268 .64 RPM
bodymap2_liver 0 .13 RPM 125 .01 RPM
bodymap2_lung 0 .02 RPM 411 .16 RPM
bodymap2_lymph_node 0 .00 RPM 414 .78 RPM
bodymap2_ovary 0 .15 RPM 474 .73 RPM
bodymap2_prostate 0 .12 RPM 360 .76 RPM
bodymap2_skeletal_muscle 0 .00 RPM 156 .20 RPM
bodymap2_testis 0 .41 RPM 351 .48 RPM
bodymap2_thyroid 0 .11 RPM 334 .99 RPM
bodymap2_white_blood_cells 0 .08 RPM 467 .98 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1624 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1624 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1624 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1624 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1624 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000113962 retrocopies
retro_btau_1084, retro_btau_1142,
Canis familiaris ENSCAFG000000055041 retrocopy
retro_cfam_1140,
Homo sapiens ENSG00000092199 2 retrocopies
retro_hsap_1624 , retro_hsap_3740,
Homo sapiens ENSG000001259701 retrocopy
retro_hsap_37,
Gorilla gorilla ENSGGOG000000230151 retrocopy
retro_ggor_1046,
Microcebus murinus ENSMICG000000076822 retrocopies
retro_mmur_1439, retro_mmur_863,
Macaca mulatta ENSMMUG000000148094 retrocopies
retro_mmul_1112, retro_mmul_205, retro_mmul_468, retro_mmul_503,
Mustela putorius furoENSMPUG000000001642 retrocopies
retro_mputfur_231, retro_mputfur_241,
Mus musculus ENSMUSG000000603731 retrocopy
retro_mmus_1388,
Nomascus leucogenys ENSNLEG000000143622 retrocopies
retro_nleu_1828, retro_nleu_59,
Oryctolagus cuniculus ENSOCUG000000150291 retrocopy
retro_ocun_138,
Otolemur garnettii ENSOGAG000000125431 retrocopy
retro_ogar_165,
Pongo abelii ENSPPYG000000055936 retrocopies
retro_pabe_1116, retro_pabe_1263, retro_pabe_1342, retro_pabe_2, retro_pabe_722, retro_pabe_780,
Pan troglodytes ENSPTRG000000061182 retrocopies
retro_ptro_1089, retro_ptro_2539,
Rattus norvegicus ENSRNOG000000116211 retrocopy
retro_rnor_922,
Tupaia belangeri ENSTBEG0000001151411 retrocopies
retro_tbel_1738, retro_tbel_2114, retro_tbel_2475, retro_tbel_2838, retro_tbel_2849, retro_tbel_3094, retro_tbel_3293, retro_tbel_3776, retro_tbel_3903, retro_tbel_3937, retro_tbel_818,
Tarsius syrichta ENSTSYG000000033053 retrocopies
retro_tsyr_1004, retro_tsyr_1326, retro_tsyr_1411,
Tursiops truncatus ENSTTRG000000160552 retrocopies
retro_ttru_1299, retro_ttru_1490,

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 = 0.15 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 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 .07 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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