RetrogeneDB ID:

retro_hsap_4257

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:42491164..42492067(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000227069
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CNN2
Ensembl ID:ENSG00000064666
Aliases:None
Description:calponin 2 [Source:HGNC Symbol;Acc:2156]


Retrocopy-Parental alignment summary:






>retro_hsap_4257
GTAAGCTCCACGCAGTTCAACAAGGGCCCCTCCTACAGGCTCTTGGCGGACGTCCAGAACAGGCTTCTGCCCAAATATGA
CTCCCAGAAGGAGGCAGAGCTCCGCAGCTGGATCAAGGGATTCACTGGCCTCTCCATCCGCCCCGACTTCCAGAAGGGCC
TGAAGGACGGGATTATTTTATGCACACTCGTGAACAAACTGCAGCCGGGCTCAGTCCCCAAGATCAACGGCTTCCGTGTA
GAACTGGCACTAGCTAGAAAACCTCTCCAACTTCCTCAAGGCAATGGTCAGCTACGGCATGATCCCGTGGACCTATTTGA
GGCCAACAACCTGTTTGAGAGTGGGAACAATATGCAGGTGCGGGTGTCTCTTCTCGCCCTGGCAGGGAAGGCCAAGACTA
AGGGGCTGCGGAGCGGGGTGGACATCCGTGACAAGTACTCAGAGAAGCAGAACTTCGACGACACCACCATGAAGGCCAGC
CAGTGCGTCATCCGGCTGCAGATTACCAACAAATGTGCCAGCCAGTCAGGCATGACCGCATATGGCACGAGGAGGCATCT
CTACGACCCCAAGAACCGCATCCTGCCCCCCATGGACAATTCGACCATCAGCCTCCAGATGGGTACAAACAAGTGCGCCA
GCCAGGTGGGCATGACGGCTCCCGGGACCCAGCGGCACATCTATGACACCAAGTTGGGAATCGACAAGTGTGAGAACTCC
TCCATGTCCCTGAAGATGGGCTACACGTAGGTTGCCAATCACAGCGGCCAGGTCTTTGGCCTAGGCCGGCAAATATACGA
ACCCAAGTACTAGCCAGGTGGCCCAGTGGCCCACGGGGCTCCCTCCGCCGGCAACTGCCCAGGGCCAGGGGAGGCCCCTT
ACTACCAGGAGGAGACCGGCTAC

ORF - retro_hsap_4257 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.03 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGPDFQKGLKDGTILCTLMNKLQPG
.SSTQFNKGPSY.L.A.V.NRLL.KYD.QKEAELR.WI.G.TGLSI.PDFQKGLKDG.ILCTL.NKLQPG
RetrocopyVSSTQFNKGPSYRLLADVQNRLLPKYDSQKEAELRSWIKGFTGLSIRPDFQKGLKDGIILCTLVNKLQPG
ParentalSVPKIN-RSMQNWHQLENLSNFIKAMVSYGM-NPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGLQS
SVPKIN..S..NWH.LENLSNF.KAMVSYGM..PVDLFEAN.LFESGN..QV.VSLLALAGKAKTKGL.S
RetrocopySVPKIN>ASV*NWH*LENLSNFLKAMVSYGM<DPVDLFEANNLFESGNNMQVRVSLLALAGKAKTKGLRS
ParentalGVDIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISL
GVDI..KYSEKQ..NFDD.TMKA.QCVI.LQ..TNKCASQSGMTAYGTRRHLYDPKN.ILPPMD.STISL
RetrocopyGVDIRDKYSEKQ--NFDDTTMKASQCVIRLQI-TNKCASQSGMTAYGTRRHLYDPKNRILPPMDNSTISL
ParentalQMGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYCPQGT
QMGTNKCASQVGMTAPGT.RHIYDTKLG.DKC.NSSMSL.MGYT..AN.SGQVFGLGRQIY.PKY.P.G.
RetrocopyQMGTNKCASQVGMTAPGTQRHIYDTKLGIDKCENSSMSLKMGYT*VANHSGQVFGLGRQIYEPKY*PGGP
ParentalVADGAPSGTGDCPDPGEVPEYPPYYQEEAGY
VA.GAPS..G.CP.PGE.P....YYQEE.GY
RetrocopyVAHGAPS-AGNCPGPGEAP----YYQEETGY

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 .12 RPM 112 .57 RPM
bodymap2_adrenal 0 .00 RPM 74 .98 RPM
bodymap2_brain 0 .00 RPM 7 .85 RPM
bodymap2_breast 0 .00 RPM 71 .30 RPM
bodymap2_colon 0 .00 RPM 53 .46 RPM
bodymap2_heart 0 .04 RPM 21 .03 RPM
bodymap2_kidney 0 .00 RPM 45 .66 RPM
bodymap2_liver 0 .00 RPM 12 .93 RPM
bodymap2_lung 0 .00 RPM 217 .30 RPM
bodymap2_lymph_node 0 .00 RPM 138 .72 RPM
bodymap2_ovary 0 .00 RPM 182 .32 RPM
bodymap2_prostate 0 .00 RPM 86 .83 RPM
bodymap2_skeletal_muscle 0 .00 RPM 7 .91 RPM
bodymap2_testis 0 .00 RPM 39 .76 RPM
bodymap2_thyroid 0 .00 RPM 73 .44 RPM
bodymap2_white_blood_cells 0 .00 RPM 341 .88 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4257 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4257 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4257 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4257 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4257 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 7 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000064666 16 retrocopies
retro_hsap_1168, retro_hsap_1575, retro_hsap_1697, retro_hsap_2127, retro_hsap_2495, retro_hsap_255, retro_hsap_2576, retro_hsap_2764, retro_hsap_3505, retro_hsap_4168, retro_hsap_4170, retro_hsap_4175, retro_hsap_4257 , retro_hsap_4269, retro_hsap_4326, retro_hsap_943,
Homo sapiens ENSG000001175191 retrocopy
retro_hsap_3419,
Homo sapiens ENSG000001587101 retrocopy
retro_hsap_4108,
Gorilla gorilla ENSGGOG000000281539 retrocopies
retro_ggor_1199, retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Macaca mulatta ENSMMUG000000153061 retrocopy
retro_mmul_1131,
Mus musculus ENSMUSG000000046652 retrocopies
retro_mmus_1824, retro_mmus_2317,
Pongo abelii ENSPPYG0000000930212 retrocopies
retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,

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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