RetrogeneDB ID:

retro_hsap_3882

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:99040508..99041119(-)
Located in intron of:ENSG00000160917
Retrocopy
information
Ensembl ID:ENSG00000228335
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SARNP
Ensembl ID:ENSG00000205323
Aliases:SARNP, CIP29, HCC1, HSPC316, THO1
Description:SAP domain containing ribonucleoprotein [Source:HGNC Symbol;Acc:24432]


Retrocopy-Parental alignment summary:






>retro_hsap_3882
ATGGTAACTGAGATGGTGGAGCTCCATAAGCTGAAGCTTGCTAAACTAAAGCAAGAATGTCTTCTTGTGGTTTGGAGACC
AAGGGAATAAAGCAAGATCTTATCCACAGACTCCAGGCATATCTTGAAGAACATGCTGAAGAGGAGGCAAATGAAGATGT
ACTAGGAGATGAAACAGAAGAAGAAAAAAACCCCTTGTCAAATAGGAAGAACCCCCTGAAAAAAACTGTTGATGTGGCAG
CAGAGAAGAAAGTGGTGAAAATTACATCTGAAATACCACAGGCTGAGAGAATGCAGAAGAGGGCCGAACAATTCAGTGTA
CCTGTGAGCTTGGAGAGTAAGAAAGCTGCTCAGGCAGCTAGGTTTGGGATTTCTTCAGTTCCAACAAAAGTCTGTCATCT
GAACACACCTATGGTTAACTTGGATAAGCCGAAGGAAAGAGCTCAAAGATTTGGTTTGAATGTCTCTTCAATTTCCAGAA
AGTCTGAAGATGATAAGAAACTGAAAAAGAGGAAGGAGCGATTTGGGATTGTCACAAGTTCAGCTGGAACTGGAACCACA
GAGGATACAGAGGCAAAGAAGAGGAAAAGAGCAGAGCGCTTTGGCATTGCC

ORF - retro_hsap_3882 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.85 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMATETVELHKLKLAELKQECL-ARGLETKGIKQDLIHRLQAYLEEHAEEEANEEDVLGDETEEEET-KPI
M.TE.VELHKLKLA.LKQECL...GLETKGIKQDLIHRLQAYLEEHAEEEANE.DVLGDET.EEE..KP.
RetrocopyMVTEMVELHKLKLAKLKQECL<SCGLETKGIKQDLIHRLQAYLEEHAEEEANE-DVLGDET-EEEK<KPL
ParentalELPVKEEEPPEK-TVDVAAEKKVVKITSEIPQTERMQKRAERFNVPVSLESKKAARAARFGISSVPTKGL
...VK.EEPPEK.TVDVAAEKKVVKITSEIPQ.ERMQKRAE.F.VPVSLESKKAA.AARFGISSVPTK..
Retrocopy---VK*EEPPEK>TVDVAAEKKVVKITSEIPQAERMQKRAEQFSVPVSLESKKAAQAARFGISSVPTK-V
ParentalSSDNKPMVNLDKLKERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGTGTTEDTEAKKRKRAERF
...N.PMVNLDK.KERAQRFGLNVSSISRKSEDD.KLKKRKERFGIVTSSAGTGTTEDTEAKKRKRAERF
RetrocopyCHLNTPMVNLDKPKERAQRFGLNVSSISRKSEDDKKLKKRKERFGIVTSSAGTGTTEDTEAKKRKRAERF
ParentalGIA
GIA
RetrocopyGIA

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 .56 RPM 1 .97 RPM
bodymap2_adrenal 0 .92 RPM 3 .56 RPM
bodymap2_brain 0 .59 RPM 2 .86 RPM
bodymap2_breast 0 .51 RPM 1 .69 RPM
bodymap2_colon 0 .52 RPM 2 .75 RPM
bodymap2_heart 0 .18 RPM 2 .10 RPM
bodymap2_kidney 0 .02 RPM 2 .96 RPM
bodymap2_liver 0 .09 RPM 0 .46 RPM
bodymap2_lung 0 .21 RPM 5 .19 RPM
bodymap2_lymph_node 0 .38 RPM 4 .53 RPM
bodymap2_ovary 0 .96 RPM 4 .14 RPM
bodymap2_prostate 0 .71 RPM 6 .96 RPM
bodymap2_skeletal_muscle 0 .42 RPM 0 .58 RPM
bodymap2_testis 0 .34 RPM 4 .34 RPM
bodymap2_thyroid 0 .83 RPM 2 .47 RPM
bodymap2_white_blood_cells 0 .16 RPM 1 .79 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_3882 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3882 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3882 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3882 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3882 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2644
Gorilla gorilla retro_ggor_2613
Pongo abelii retro_pabe_3116
Parental genes homology:
Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000117692 retrocopies
retro_amel_1602, retro_amel_347,
Bos taurus ENSBTAG000000206621 retrocopy
retro_btau_202,
Callithrix jacchus ENSCJAG000000078538 retrocopies
retro_cjac_1070, retro_cjac_1487, retro_cjac_1801, retro_cjac_2439, retro_cjac_2560, retro_cjac_389, retro_cjac_4139, retro_cjac_731,
Cavia porcellus ENSCPOG000000117551 retrocopy
retro_cpor_1313,
Dipodomys ordii ENSDORG000000010651 retrocopy
retro_dord_80,
Erinaceus europaeus ENSEEUG000000151761 retrocopy
retro_eeur_549,
Homo sapiens ENSG00000205323 1 retrocopy
retro_hsap_3882 ,
Gorilla gorilla ENSGGOG000000132172 retrocopies
retro_ggor_2613, retro_ggor_2753,
Loxodonta africana ENSLAFG000000150531 retrocopy
retro_lafr_1024,
Microcebus murinus ENSMICG000000109021 retrocopy
retro_mmur_358,
Monodelphis domestica ENSMODG000000289491 retrocopy
retro_mdom_1909,
Mustela putorius furoENSMPUG000000008851 retrocopy
retro_mputfur_617,
Mus musculus ENSMUSG000000784271 retrocopy
retro_mmus_54,
Nomascus leucogenys ENSNLEG000000175992 retrocopies
retro_nleu_2779, retro_nleu_569,
Procavia capensis ENSPCAG000000094772 retrocopies
retro_pcap_262, retro_pcap_45,
Pongo abelii ENSPPYG000000046302 retrocopies
retro_pabe_3116, retro_pabe_3358,
Pan troglodytes ENSPTRG000000297472 retrocopies
retro_ptro_2644, retro_ptro_2782,
Rattus norvegicus ENSRNOG000000305202 retrocopies
retro_rnor_1326, retro_rnor_471,

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 = 0.5 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .24 RPM
CEU_NA11843 0 .31 RPM
CEU_NA11930 0 .26 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .21 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .31 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .19 RPM
FIN_HG00277 0 .26 RPM
FIN_HG00315 0 .25 RPM
FIN_HG00321 0 .18 RPM
FIN_HG00328 0 .17 RPM
FIN_HG00338 0 .21 RPM
FIN_HG00349 0 .17 RPM
FIN_HG00375 0 .34 RPM
FIN_HG00377 0 .38 RPM
FIN_HG00378 0 .21 RPM
GBR_HG00099 0 .09 RPM
GBR_HG00111 0 .37 RPM
GBR_HG00114 0 .26 RPM
GBR_HG00119 0 .22 RPM
GBR_HG00131 0 .20 RPM
GBR_HG00133 0 .34 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .33 RPM
GBR_HG00142 0 .31 RPM
GBR_HG00143 0 .29 RPM
TSI_NA20512 0 .34 RPM
TSI_NA20513 0 .29 RPM
TSI_NA20518 0 .22 RPM
TSI_NA20532 0 .27 RPM
TSI_NA20538 0 .23 RPM
TSI_NA20756 0 .23 RPM
TSI_NA20765 0 .19 RPM
TSI_NA20771 0 .14 RPM
TSI_NA20786 0 .13 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .20 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .21 RPM
YRI_NA19093 0 .29 RPM
YRI_NA19099 0 .32 RPM
YRI_NA19114 0 .24 RPM
YRI_NA19118 0 .25 RPM
YRI_NA19213 0 .19 RPM
YRI_NA19214 0 .20 RPM
YRI_NA19223 0 .50 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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