RetrogeneDB ID:

retro_hsap_2244

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:35444445..35444670(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000196085
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SMIM7
Ensembl ID:ENSG00000214046
Aliases:SMIM7, C19orf42
Description:small integral membrane protein 7 [Source:HGNC Symbol;Acc:28419]


Retrocopy-Parental alignment summary:






>retro_hsap_2244
ATGATTGGAGACATCCTGCTATTTGGGACATTGCTGATGAATGCTGGGGCAGTGCTCAACTTTAAGCTGAAAAAGAAGGA
CATGCAGGGCTTTGGGAAGGAGGCATGGGAGCCCAGCACAGGTGACAACACGAGGGAATTCTTACTGAGCCTCAGATACT
TTTGAATCTTCACCATCCTGTGGAACGTCTTCATCATGTGCTGCATGATTGTGCTGTTTGGCTCC

ORF - retro_hsap_2244 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.33 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMIGDILLFGTLLMNAGAVLNFKLKKKDTQGFGEESREPSTGDNIREFLLSLRYFRIFIALWNIFMMFCMI
MIGDILLFGTLLMNAGAVLNFKLKKKD.QGFG.E..EPSTGDN.REFLLSLRYF.IF..LWN.F.M.CMI
RetrocopyMIGDILLFGTLLMNAGAVLNFKLKKKDMQGFGKEAWEPSTGDNTREFLLSLRYF*IFTILWNVFIMCCMI
ParentalVLFGS
VLFGS
RetrocopyVLFGS

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 31 .21 RPM
bodymap2_adrenal 0 .00 RPM 66 .73 RPM
bodymap2_brain 0 .00 RPM 30 .10 RPM
bodymap2_breast 0 .00 RPM 53 .39 RPM
bodymap2_colon 0 .00 RPM 29 .60 RPM
bodymap2_heart 0 .00 RPM 14 .88 RPM
bodymap2_kidney 0 .00 RPM 40 .95 RPM
bodymap2_liver 0 .00 RPM 28 .20 RPM
bodymap2_lung 0 .00 RPM 23 .86 RPM
bodymap2_lymph_node 0 .00 RPM 28 .65 RPM
bodymap2_ovary 0 .00 RPM 43 .76 RPM
bodymap2_prostate 0 .00 RPM 38 .19 RPM
bodymap2_skeletal_muscle 0 .00 RPM 10 .06 RPM
bodymap2_testis 0 .00 RPM 39 .27 RPM
bodymap2_thyroid 0 .00 RPM 53 .14 RPM
bodymap2_white_blood_cells 0 .00 RPM 26 .17 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2244 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2244 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2244 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2244 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2244 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1589
Pongo abelii retro_pabe_1964
Parental genes homology:
Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101051 retrocopy
retro_amel_1688,
Canis familiaris ENSCAFG000000156431 retrocopy
retro_cfam_1927,
Callithrix jacchus ENSCJAG000000139361 retrocopy
retro_cjac_1223,
Equus caballus ENSECAG000000268611 retrocopy
retro_ecab_640,
Felis catus ENSFCAG000000164111 retrocopy
retro_fcat_934,
Homo sapiens ENSG00000214046 1 retrocopy
retro_hsap_2244 ,
Mus musculus ENSMUSG000000446001 retrocopy
retro_mmus_450,
Nomascus leucogenys ENSNLEG000000055691 retrocopy
retro_nleu_1315,
Pongo abelii ENSPPYG000000096942 retrocopies
retro_pabe_1964, retro_pabe_2031,
Pan troglodytes ENSPTRG000000106501 retrocopy
retro_ptro_1589,
Rattus norvegicus ENSRNOG000000420371 retrocopy
retro_rnor_2694,
Sus scrofa ENSSSCG000000138631 retrocopy
retro_sscr_955,
Tarsius syrichta ENSTSYG000000095561 retrocopy
retro_tsyr_1550,
Tursiops truncatus ENSTTRG000000150202 retrocopies
retro_ttru_136, retro_ttru_597,
Vicugna pacos ENSVPAG000000066991 retrocopy
retro_vpac_65,

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).





Copyright © RetrogeneDB 2014-2017