RetrogeneDB ID:

retro_hsap_189

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:96856228..96856797(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225923
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SCAMP1
Ensembl ID:ENSG00000085365
Aliases:SCAMP1, SCAMP, SCAMP37
Description:secretory carrier membrane protein 1 [Source:HGNC Symbol;Acc:10563]


Retrocopy-Parental alignment summary:






>retro_hsap_189
CCTCCACCAGGCAGTGTGAGGATGCCTAACATACCCAATACACAACCAGCAATAATGAAACCAACAGAGAAACATCCAGT
TTATACGCTGATTGCAAAAAAACATGCATTGGCCCAAGCTGAACTTAAACACCAGGAAGAAGTAGAAAGAAAAGATGCAG
AATTAGTCATCGGGAATGAGAAATGCAAAACCTCACTCAACATGGTAGAAAAAATAATTGGCCACTTCTTCTTAGCAATT
TTCCTATAGAACCTTGTTTCTATCAGGATTTTTCTGTTGACATTCCTATAGAATTCCAAAAGACAGTAAAGCTTATATAC
TACTTGTGGATGTTCCATGCTGTAACACTATTTCTAAATATCTTCAGATGCTTGTCTTGGTTTTGTGTTGATTTTGCAAG
AGTGGTTGATTTTAGTTTGAGTATCCTGTGGTTCTTGCTTTTTACTCCTTGTTAATTTGTCTGTTGGTACAGATCACTTT
ATGGAGCTTTCAGGAGTGGCAGTTCATTCAGACTCTTTGTATTCTTCTTCGTCTATATTTGTTAGTTTGCTGTACATGCA
TTCCAGGCA

ORF - retro_hsap_189 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.29 %
Parental protein coverage: 56.51 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPPPGGVKMPNVPNTQPAIMKPTEEHPAYTQIAKEHALAQAELLKRQEELERKAAEL-DRREREMQNLSQH
PPPG.V.MPN.PNTQPAIMKPTE.HP.YT.IAK.HALAQAEL.K.QEE.ERK.AEL...RE.EMQNL.QH
RetrocopyPPPGSVRMPNIPNTQPAIMKPTEKHPVYTLIAKKHALAQAEL-KHQEEVERKDAEL<SHRE*EMQNLTQH
ParentalGRKNNWPPLPSNFPVGPCFYQDFSVDIPVEFQKTVKLMYYLWMFHAVTLFLNIFGCLAWFCVDSARAVDF
GRKNNWP.L.SNFP..PCFYQDFSVDIP.EFQKTVKL.YYLWMFHAVTLFLNIF.CL.WFCVD.AR.VDF
RetrocopyGRKNNWPLLLSNFPIEPCFYQDFSVDIPIEFQKTVKLIYYLWMFHAVTLFLNIFRCLSWFCVDFARVVDF
ParentalGLSILWFLLFTPCSFVCWYRPLYGAFRSDSSFRFFVFFFVYICQFAVHVLQA
.LSILWFLLFTPC.FVCWYR.LYGAFRS.SSFR.FVFFFVYIC.FAVH..QA
RetrocopySLSILWFLLFTPC*FVCWYRSLYGAFRSGSSFRLFVFFFVYIC*FAVHAFQA

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 82 .63 RPM
bodymap2_adrenal 0 .00 RPM 39 .77 RPM
bodymap2_brain 0 .00 RPM 211 .64 RPM
bodymap2_breast 0 .00 RPM 63 .87 RPM
bodymap2_colon 0 .00 RPM 111 .08 RPM
bodymap2_heart 0 .00 RPM 46 .78 RPM
bodymap2_kidney 0 .00 RPM 90 .81 RPM
bodymap2_liver 0 .00 RPM 18 .17 RPM
bodymap2_lung 0 .00 RPM 66 .70 RPM
bodymap2_lymph_node 0 .00 RPM 52 .72 RPM
bodymap2_ovary 0 .00 RPM 74 .93 RPM
bodymap2_prostate 0 .00 RPM 103 .40 RPM
bodymap2_skeletal_muscle 0 .00 RPM 36 .05 RPM
bodymap2_testis 0 .09 RPM 74 .38 RPM
bodymap2_thyroid 0 .00 RPM 91 .03 RPM
bodymap2_white_blood_cells 0 .00 RPM 66 .05 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_189 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_189 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_189 retrocopy 5' end.

Lab - click to see more details

retro_hsap_189 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_189 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_269
Macaca mulatta retro_mmul_396
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000323951 retrocopy
retro_cfam_227,
Cavia porcellus ENSCPOG000000088681 retrocopy
retro_cpor_174,
Homo sapiens ENSG00000085365 1 retrocopy
retro_hsap_189 ,
Gorilla gorilla ENSGGOG000000151911 retrocopy
retro_ggor_269,
Macaca mulatta ENSMMUG000000163981 retrocopy
retro_mmul_396,
Monodelphis domestica ENSMODG000000197311 retrocopy
retro_mdom_964,
Nomascus leucogenys ENSNLEG000000127751 retrocopy
retro_nleu_1000,
Tarsius syrichta ENSTSYG000000141131 retrocopy
retro_tsyr_1676,

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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