RetrogeneDB ID:

retro_hsap_2715

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:145402358..145402654(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000241695
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GM2A
Ensembl ID:ENSG00000196743
Aliases:GM2A, GM2-AP, SAP-3
Description:GM2 ganglioside activator [Source:HGNC Symbol;Acc:4367]


Retrocopy-Parental alignment summary:






>retro_hsap_2715
CAATCCCTGACGCAGACTTCGCTCCAGATCGCCCTGGGCTTGCTTCTCGCGCCCCTGTGCAAGCCCACCTGAAAAAGCTC
AGTAGCTTTTCCTGGAATAACTGTGATGAAGGGAAGGACCCTGCGGTGATCAGAGGCGTAACTCTGGAGCCTGACCCCAT
CATTCTTCCGGAGAACGTGACCCTCAGTCTCCTGGGCAGCACCACTGTCTCCCTGAGTTCTCGTCTGGAGATGGATTTAG
TTTTGGAGAAGGAAGTGGCTGGCCCCTGGATCAAGACCCCATGGCAGCTGTACCTT

ORF - retro_hsap_2715 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.79 %
Parental protein coverage: 52.85 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQSLMQAPLLIALGLLLA-APAQAHLKKPSQLSSFSWDNCDEGKDPAVIRSLTLEPDPIIVPGNVTLSVMG
QSL.Q..L.IALGLLLA.AP.QAHLKK...LSSFSW.NCDEGKDPAVIR..TLEPDPII.P.NVTLS..G
RetrocopyQSLTQTSLQIALGLLLA<APVQAHLKK---LSSFSWNNCDEGKDPAVIRGVTLEPDPIILPENVTLSLLG
ParentalSTSVPLSSPLKVDLVLEKEVAGLWIKIPCTDYI
ST.V.LSS.L..DLVLEKEVAG.WIK.P...Y.
RetrocopySTTVSLSSRLEMDLVLEKEVAGPWIKTPWQLYL

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 46 .93 RPM
bodymap2_adrenal 0 .00 RPM 65 .79 RPM
bodymap2_brain 0 .00 RPM 81 .67 RPM
bodymap2_breast 0 .00 RPM 116 .89 RPM
bodymap2_colon 0 .00 RPM 40 .26 RPM
bodymap2_heart 0 .00 RPM 52 .95 RPM
bodymap2_kidney 0 .00 RPM 27 .96 RPM
bodymap2_liver 0 .00 RPM 26 .19 RPM
bodymap2_lung 0 .00 RPM 64 .01 RPM
bodymap2_lymph_node 0 .00 RPM 60 .07 RPM
bodymap2_ovary 0 .00 RPM 62 .65 RPM
bodymap2_prostate 0 .00 RPM 71 .84 RPM
bodymap2_skeletal_muscle 0 .00 RPM 12 .57 RPM
bodymap2_testis 0 .00 RPM 49 .89 RPM
bodymap2_thyroid 0 .00 RPM 30 .34 RPM
bodymap2_white_blood_cells 0 .00 RPM 116 .89 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2715 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2715 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2715 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2715 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2715 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1834
Gorilla gorilla retro_ggor_1891
Parental genes homology:
Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG000000205871 retrocopy
retro_ecab_510,
Homo sapiens ENSG00000196743 2 retrocopies
retro_hsap_264, retro_hsap_2715 ,
Gorilla gorilla ENSGGOG000000153022 retrocopies
retro_ggor_1891, retro_ggor_313,
Macropus eugenii ENSMEUG000000104211 retrocopy
retro_meug_1818,
Microcebus murinus ENSMICG000000006901 retrocopy
retro_mmur_518,
Myotis lucifugus ENSMLUG000000032151 retrocopy
retro_mluc_920,
Macaca mulatta ENSMMUG000000228691 retrocopy
retro_mmul_454,
Nomascus leucogenys ENSNLEG000000109661 retrocopy
retro_nleu_866,
Oryctolagus cuniculus ENSOCUG000000158371 retrocopy
retro_ocun_704,
Ochotona princeps ENSOPRG000000061711 retrocopy
retro_opri_1169,
Pongo abelii ENSPPYG000000159621 retrocopy
retro_pabe_403,
Pan troglodytes ENSPTRG000000174312 retrocopies
retro_ptro_1834, retro_ptro_221,
Ictidomys tridecemlineatus ENSSTOG000000285001 retrocopy
retro_itri_759,
Tursiops truncatus ENSTTRG000000005031 retrocopy
retro_ttru_488,

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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