RetrogeneDB ID:

retro_hsap_98

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:55600668..55601415(+)
Located in intron of:ENSG00000087253
Retrocopy
information
Ensembl ID:ENSG00000256812
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CAPNS1
Ensembl ID:ENSG00000126247
Aliases:CAPNS1, 30K, CALPAIN4, CANP, CANPS, CAPN4, CDPS, CSS1
Description:calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]


Retrocopy-Parental alignment summary:






>retro_hsap_98
ATGTTTCTTGCAAAGGCTCTATTGGAAGGAGCAGATCGAGGTCTTGGAGAAGCTCTTGGAGGCCTCTTTGGAGGAGGTGG
TCAGAGAAGAGAAGGAGGAGGAAGAAATATTGGAGGGATAGTTGGAGGAATTGTGAATTTTATCAGTGAGGCTGCAGCAG
CTCAGTATACTCCAGAACCGCCTCCCACTCAGCAGCATTTCACCAGTGTGGAGGCCTCAGAAAGTGAGGAAGTTAGGCGA
TTTCGGCAACAATTTACACAGCTGGCTGGACCAGACATGGAGGTGGGTGCCACTGATCTGATGAATATTCTCAACAAAGT
CCTTTCTAAGCACAAAGATCTTAAGACTGACGGTTTTAGTCTTGACACCTGCCGGAGCATTGTGTCTGTCATGGACAGTG
ACACGACTGGTAAGCTGGGCTTTGAAGAATTTAAGTATCTGTGGAACAACATCAAGAAATGGCAGTGTGTTTATAAGCAG
TATGACAGGGACCATTCTGGGTCTCTGGGAAGTTCTCAGCTGCGGGGAGCTCTGCAGGCCGCAGGCTTCCAGCTAAATGA
ACAACTTTACCAAATGATTGTCCGCCGGTATGCTAATGAAGATGGAGATATGGATTTTAACAATTTCATCAGCTGCTTGG
TCCGCCTGGATGCCATGTTTCGTGCCTTCAAGTCTCTGGATAGAGATAGAGATGGCCTGATTCAAGTGTCTATCAAAGAA
TGGCTGCAGTTGACCATGTATTCCTGA

ORF - retro_hsap_98 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.77 %
Parental protein coverage: 89.93 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVLGGLISGAGGGGGGGGGGGGGGGGGGGGTAMRILGGVISAISEAAA-QYNPEPPPPRTHYSNIEANESE
.L.G...G.G...GG..GGGG....GGG.....I.GG....ISEAAA.QY.PEPPP...H....EA.ESE
RetrocopyLLEGADRGLGEALGGLFGGGGQRREGGGRNIGGIVGGIVNFISEAAAAQYTPEPPPTQQHFTSVEASESE
ParentalEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKY
EVR.FR..F.QLAG.DMEV.AT.LMNILNKV...H.DLKTDGF..DTCRS.V.VMDSDTTGKLGFEEFKY
RetrocopyEVRRFRQQFTQLAGPDMEVGATDLMNILNKVLSKHKDLKTDGFSLDTCRSIVSVMDSDTTGKLGFEEFKY
ParentalLWNNIKRWQAIYKQFDTDRSGTICSSELPGAFEAAGFHLNEHLYNMIIRRYSDESGNMDFDNFISCLVRL
LWNNIK.WQ..YKQ.D.D.SG...SS.L.GA..AAGF.LNE.LY.MI.RRY..E.G.MDF.NFISCLVRL
RetrocopyLWNNIKKWQCVYKQYDRDHSGSLGSSQLRGALQAAGFQLNEQLYQMIVRRYANEDGDMDFNNFISCLVRL
ParentalDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS
DAMFRAFKSLD.D..G.IQV.I.EWLQLTMYS
RetrocopyDAMFRAFKSLDRDRDGLIQVSIKEWLQLTMYS

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 .06 RPM 283 .40 RPM
bodymap2_adrenal 0 .06 RPM 217 .00 RPM
bodymap2_brain 0 .07 RPM 142 .05 RPM
bodymap2_breast 0 .04 RPM 270 .37 RPM
bodymap2_colon 0 .12 RPM 177 .56 RPM
bodymap2_heart 0 .04 RPM 168 .84 RPM
bodymap2_kidney 0 .21 RPM 253 .56 RPM
bodymap2_liver 0 .00 RPM 86 .50 RPM
bodymap2_lung 0 .09 RPM 294 .90 RPM
bodymap2_lymph_node 0 .11 RPM 164 .76 RPM
bodymap2_ovary 0 .08 RPM 202 .21 RPM
bodymap2_prostate 4 .40 RPM 219 .26 RPM
bodymap2_skeletal_muscle 0 .00 RPM 242 .79 RPM
bodymap2_testis 0 .15 RPM 188 .08 RPM
bodymap2_thyroid 0 .11 RPM 153 .76 RPM
bodymap2_white_blood_cells 0 .16 RPM 311 .36 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_98 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_98 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_522271694 libraries47 libraries26 libraries8 libraries54 libraries
TSS #2 TSS_522281788 libraries36 libraries4 libraries1 library0 libraries

The graphical summary, for retro_hsap_98 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_98 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_98 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1112
Gorilla gorilla retro_ggor_1241
Pongo abelii retro_pabe_1359
Macaca mulatta retro_mmul_1567
Mus musculus retro_mmus_80
Rattus norvegicus retro_rnor_1447
Bos taurus retro_btau_692
Sus scrofa retro_sscr_73
Canis familiaris retro_cfam_942
Equus caballus retro_ecab_707
Parental genes homology:
Parental genes homology involve 26 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000005111 retrocopy
retro_acar_205,
Ailuropoda melanoleuca ENSAMEG000000010241 retrocopy
retro_amel_136,
Bos taurus ENSBTAG000000148722 retrocopies
retro_btau_1126, retro_btau_692,
Canis familiaris ENSCAFG000000313141 retrocopy
retro_cfam_942,
Callithrix jacchus ENSCJAG000000095941 retrocopy
retro_cjac_2940,
Cavia porcellus ENSCPOG000000001151 retrocopy
retro_cpor_1131,
Equus caballus ENSECAG000000122101 retrocopy
retro_ecab_707,
Felis catus ENSFCAG000000141491 retrocopy
retro_fcat_1691,
Homo sapiens ENSG00000126247 1 retrocopy
retro_hsap_98 ,
Gorilla gorilla ENSGGOG000000036992 retrocopies
retro_ggor_1241, retro_ggor_263,
Myotis lucifugus ENSMLUG000000249441 retrocopy
retro_mluc_2336,
Macaca mulatta ENSMMUG000000002492 retrocopies
retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica ENSMODG000000141791 retrocopy
retro_mdom_410,
Mustela putorius furoENSMPUG000000056171 retrocopy
retro_mputfur_444,
Mus musculus ENSMUSG000000017941 retrocopy
retro_mmus_80,
Nomascus leucogenys ENSNLEG000000117122 retrocopies
retro_nleu_1328, retro_nleu_992,
Ornithorhynchus anatinus ENSOANG000000027361 retrocopy
retro_oana_113,
Pongo abelii ENSPPYG000000098982 retrocopies
retro_pabe_1359, retro_pabe_448,
Pelodiscus sinensis ENSPSIG000000127931 retrocopy
retro_psin_45,
Pan troglodytes ENSPTRG000000108872 retrocopies
retro_ptro_1112, retro_ptro_168,
Pteropus vampyrus ENSPVAG000000128853 retrocopies
retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus ENSRNOG000000457472 retrocopies
retro_rnor_1447, retro_rnor_2145,
Sorex araneus ENSSARG000000042661 retrocopy
retro_sara_215,
Sus scrofa ENSSSCG000000301492 retrocopies
retro_sscr_495, retro_sscr_73,
Ictidomys tridecemlineatus ENSSTOG000000262351 retrocopy
retro_itri_342,
Vicugna pacos ENSVPAG000000080741 retrocopy
retro_vpac_64,

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 = 0.04 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 .04 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 .03 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 .03 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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