RetrogeneDB ID:

retro_hsap_2343

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:174296079..174296540(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213148
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HN1
Ensembl ID:ENSG00000189159
Aliases:HN1, ARM2, HN1A
Description:hematological and neurological expressed 1 [Source:HGNC Symbol;Acc:14569]


Retrocopy-Parental alignment summary:






>retro_hsap_2343
ATGACCACCACCACTACCTTCAAGGGTGTTAACCCCAACAGCAGGAATAGCTCCCGGGTTTTGCGGCTGCTGGGTGGTGG
ATCCAATTTTTCATTGGGTTTTGATGAACCAACAGAACAACCTGTGAGAAAGAACAAAATGTCCTCTAGTATCTTTGGGA
CACCTGAAGAAAATCCACCTTCTTGGGCCACATTGGCAGGTGCCAAGTCTAGAGGTGGCGGAGAAGACTTGGAGTCATCC
GGACTGCAGGGAAGGAACGCTTCTGAAGCAAACTCTGCAGATTCTTAGATCTGAAGGGAGAAGGTGACATTCATGAAAAT
GTGGACACAGACTTGCAAGGCAGCCTGGGGCCGAGGGAAGAGAAGCCTGCACCTGCTGCACCTGTGCTGAGCCCCGTGGC
CCTGGCCCCAGGACCATCCATAGGAAATCCCCCTGGTGGCAAGTGCAGCCTCATCCTGGGT

ORF - retro_hsap_2343 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.58 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMTTTTTFKGVDPNSRNSSRVLRPPGGGSNFSLGFDEPTEQPVRKNKMASNIFGTPEENQASWAKSAGAKS
MTTTTTFKGV.PNSRNSSRVLR..GGGSNFSLGFDEPTEQPVRKNKM.S.IFGTPEEN..SWA..AGAKS
RetrocopyMTTTTTFKGVNPNSRNSSRVLRLLGGGSNFSLGFDEPTEQPVRKNKMSSSIFGTPEENPPSWATLAGAKS
ParentalSGGREDLESSGLQRRNSSEASSGD-FLDLKGEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVP
.GG.EDLESSGLQ.RN.SEA.S.D.FLDLKGEGDIHENVDTDL.GSLG..EEKP.PAAPV.SPVA.AP.P
RetrocopyRGGGEDLESSGLQGRNASEANSAD<FLDLKGEGDIHENVDTDLQGSLGPREEKPAPAAPVLSPVALAPGP
ParentalSRRNPPGGKSSLVLG
S..NPPGGK.SL.LG
RetrocopySIGNPPGGKCSLILG

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 7 .06 RPM
bodymap2_adrenal 0 .00 RPM 18 .85 RPM
bodymap2_brain 0 .00 RPM 22 .36 RPM
bodymap2_breast 0 .00 RPM 12 .14 RPM
bodymap2_colon 0 .00 RPM 14 .31 RPM
bodymap2_heart 0 .00 RPM 4 .87 RPM
bodymap2_kidney 0 .00 RPM 30 .73 RPM
bodymap2_liver 0 .00 RPM 11 .89 RPM
bodymap2_lung 0 .00 RPM 28 .59 RPM
bodymap2_lymph_node 0 .00 RPM 26 .04 RPM
bodymap2_ovary 0 .00 RPM 17 .41 RPM
bodymap2_prostate 0 .00 RPM 15 .09 RPM
bodymap2_skeletal_muscle 0 .00 RPM 19 .10 RPM
bodymap2_testis 0 .08 RPM 97 .81 RPM
bodymap2_thyroid 0 .00 RPM 8 .47 RPM
bodymap2_white_blood_cells 0 .00 RPM 71 .76 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_2343 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2343 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2343 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2343 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2343 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1715
Gorilla gorilla retro_ggor_1780
Callithrix jacchus retro_cjac_2715
Parental genes homology:
Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000145531 retrocopy
retro_cjac_2715,
Echinops telfairi ENSETEG000000132941 retrocopy
retro_etel_89,
Homo sapiens ENSG00000189159 1 retrocopy
retro_hsap_2343 ,
Gorilla gorilla ENSGGOG000000139961 retrocopy
retro_ggor_1780,
Mustela putorius furoENSMPUG000000139711 retrocopy
retro_mputfur_1200,
Mus musculus ENSMUSG000000207376 retrocopies
retro_mmus_1096, retro_mmus_2442, retro_mmus_2574, retro_mmus_3706, retro_mmus_864, retro_mmus_934,
Nomascus leucogenys ENSNLEG000000006101 retrocopy
retro_nleu_348,
Oryctolagus cuniculus ENSOCUG000000029502 retrocopies
retro_ocun_1647, retro_ocun_457,
Ochotona princeps ENSOPRG000000108872 retrocopies
retro_opri_537, retro_opri_88,
Pan troglodytes ENSPTRG000000242461 retrocopy
retro_ptro_1715,
Rattus norvegicus ENSRNOG000000036612 retrocopies
retro_rnor_1794, retro_rnor_454,
Ictidomys tridecemlineatus ENSSTOG000000151711 retrocopy
retro_itri_1449,

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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