RetrogeneDB ID:

retro_hsap_2900

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:188707249..188707717(-)
Located in intron of:ENSG00000188001
Retrocopy
information
Ensembl ID:ENSG00000236182
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ENOPH1
Ensembl ID:ENSG00000145293
Aliases:ENOPH1, E1, MASA, MST145, mtnC
Description:enolase-phosphatase 1 [Source:HGNC Symbol;Acc:24599]


Retrocopy-Parental alignment summary:






>retro_hsap_2900
GGGAATGGAGTGGATGATCTGCAACAGATGATCCAGGCCGTGGTAGATAAGGTGTGCTGGCAGATGTCCCTGGACGGAAA
GACCACCATGTTCAAACAGCTGCAGGACCACACGTGAAGGGCAGCATTCACAGCTCGGCCCATGAAAGCGGAGTTCTTTG
CAGATGTGTTTCCAGCAGTCAGGAAGTGGAAAGAGGCTGGAATGAAGGTGTATATCTATTCCTCTGGGAGTGTAGAGGCA
CAGAAACTGTTATTCGGGCAGTCTGCGAAGGGAAAGATTCTTGAGCTTGTTGATGGTCCCTTTGATACCAAGATTGGACA
CAAAGTAGAGAATGAAAGTTATCAAAGGATTGCAGACTGCACTGGGGGCTCAACCAACAACATTTTGTTTCTGACAGATG
TTACTCAAGAGGCCAGTGCTGCTGAGGAAGCAGATGTGCACGTAGCGGTGGTGGTGAGACTTGGAGAC

ORF - retro_hsap_2900 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.97 %
Parental protein coverage: 59.77 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGNGVDDLQQMIQAVVDNVCWQMSLDRKTTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKV
GNGVDDLQQMIQAVVD.VCWQMSLD.KTT..KQLQ.H..RAAFTA..MKAEFFADV.PAVRKW.EAGMKV
RetrocopyGNGVDDLQQMIQAVVDKVCWQMSLDGKTTMFKQLQDHT*RAAFTARPMKAEFFADVFPAVRKWKEAGMKV
ParentalYIYSSGSVEAQKLLFGHSTEGDILELVDGHFDTKIGHKVESESYRKIADSIGCSTNNILFLTDVTREASA
YIYSSGSVEAQKLLFG.S..G.ILELVDG.FDTKIGHKVE.ESY..IAD..G.STNNILFLTDVT.EASA
RetrocopyYIYSSGSVEAQKLLFGQSAKGKILELVDGPFDTKIGHKVENESYQRIADCTGGSTNNILFLTDVTQEASA
ParentalAEEADVHVAVVVRPGN
AEEADVHVAVVVR.G.
RetrocopyAEEADVHVAVVVRLGD

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 .04 RPM 16 .36 RPM
bodymap2_adrenal 0 .00 RPM 34 .59 RPM
bodymap2_brain 0 .00 RPM 106 .00 RPM
bodymap2_breast 0 .08 RPM 19 .63 RPM
bodymap2_colon 0 .00 RPM 28 .73 RPM
bodymap2_heart 0 .00 RPM 14 .01 RPM
bodymap2_kidney 0 .00 RPM 40 .78 RPM
bodymap2_liver 0 .04 RPM 15 .78 RPM
bodymap2_lung 0 .00 RPM 29 .82 RPM
bodymap2_lymph_node 0 .00 RPM 30 .02 RPM
bodymap2_ovary 0 .00 RPM 31 .77 RPM
bodymap2_prostate 0 .00 RPM 35 .52 RPM
bodymap2_skeletal_muscle 0 .00 RPM 8 .31 RPM
bodymap2_testis 0 .00 RPM 22 .83 RPM
bodymap2_thyroid 0 .04 RPM 31 .88 RPM
bodymap2_white_blood_cells 0 .00 RPM 34 .47 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2900 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2900 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2900 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2900 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2900 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1960
Gorilla gorilla retro_ggor_2010
Pongo abelii retro_pabe_2399
Parental genes homology:
Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000051402 retrocopies
retro_amel_1186, retro_amel_930,
Choloepus hoffmanni ENSCHOG000000032834 retrocopies
retro_chof_2150, retro_chof_470, retro_chof_486, retro_chof_596,
Callithrix jacchus ENSCJAG000000152512 retrocopies
retro_cjac_1376, retro_cjac_2375,
Equus caballus ENSECAG000000196121 retrocopy
retro_ecab_164,
Erinaceus europaeus ENSEEUG000000042741 retrocopy
retro_eeur_563,
Homo sapiens ENSG00000145293 1 retrocopy
retro_hsap_2900 ,
Gorilla gorilla ENSGGOG000000037191 retrocopy
retro_ggor_2010,
Loxodonta africana ENSLAFG000000086191 retrocopy
retro_lafr_1158,
Macropus eugenii ENSMEUG000000114581 retrocopy
retro_meug_1125,
Myotis lucifugus ENSMLUG000000144601 retrocopy
retro_mluc_2504,
Otolemur garnettii ENSOGAG000000025021 retrocopy
retro_ogar_1549,
Pongo abelii ENSPPYG000000148871 retrocopy
retro_pabe_2399,
Pan troglodytes ENSPTRG000000162181 retrocopy
retro_ptro_1960,
Tursiops truncatus ENSTTRG000000018001 retrocopy
retro_ttru_1231,

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 = 0.02 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 .02 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 .02 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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