RetrogeneDB ID:

retro_hsap_139

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:38010516..38010899(+)
Located in intron of:ENSG00000163877
Retrocopy
information
Ensembl ID:ENSG00000232273
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FTH1
Ensembl ID:ENSG00000167996
Aliases:FTH1, FHC, FTH, FTHL6, HFE5, PIG15, PLIF
Description:ferritin, heavy polypeptide 1 [Source:HGNC Symbol;Acc:3976]


Retrocopy-Parental alignment summary:






>retro_hsap_139
CTTCACCAATCTCATGAGGAGAGGGAACATGCCAAGAAACTGATGAAGCTGCAGAACCAATGAGGTGGCTGAATCTTCTT
CCTTCGGGACTTCAAGAAACCAGACCATGATGACTGGGAGAGCAGGCTGAATGCGATGGAGCATGCATTACATTTGGAAA
AACTTGGGAATCAGTCACTACTGGAACTGCACAAACTGGCCACCGACAAAATTACCCCCATTTGTGTGACTTCACTGAAA
CACATTACCTGAATGAGCAGGGGAAATCCATCAAGAATTGGGTGACCATGTGACCAACTTGCGCAAGATGAGGGCACCCG
AATCTGGCTTGGCAGAATATTTCTCTGACAAGCACACCCCGGGGAGACAGTGATAATGAAAGC

ORF - retro_hsap_139 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.21 %
Parental protein coverage: 83.01 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLHQSHEEREHAEKLMKLQNQRGGRIF-LQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDK
LHQSHEEREHA.KLMKLQNQ.GG.IF.L.D.KKPD.DDWES.LNAME.ALHLEK..NQSLLELHKLATDK
RetrocopyLHQSHEEREHAKKLMKLQNQ*GG*IFFLRDFKKPDHDDWESRLNAMEHALHLEKLGNQSLLELHKLATDK
Parental-NDPHLCDFIETHYLNEQVKAIK-ELGDHVTNLRKMGAPESGLAEYLFDKHT-LGDSDNES
.N.PHLCDF.ETHYLNEQ.K.IK.ELGDHVTNLRKM.APESGLAEY..DKHT..GDSDNES
Retrocopy<NYPHLCDFTETHYLNEQGKSIK<ELGDHVTNLRKMRAPESGLAEYFSDKHT>RGDSDNES

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .26 RPM 416 .48 RPM
bodymap2_adrenal 0 .96 RPM 130 .06 RPM
bodymap2_brain 0 .23 RPM 173 .50 RPM
bodymap2_breast 0 .14 RPM 294 .30 RPM
bodymap2_colon 0 .04 RPM 231 .41 RPM
bodymap2_heart 0 .07 RPM 98 .19 RPM
bodymap2_kidney 0 .08 RPM 318 .29 RPM
bodymap2_liver 0 .00 RPM 82 .81 RPM
bodymap2_lung 0 .25 RPM 442 .70 RPM
bodymap2_lymph_node 0 .09 RPM 156 .57 RPM
bodymap2_ovary 0 .17 RPM 138 .99 RPM
bodymap2_prostate 0 .10 RPM 201 .36 RPM
bodymap2_skeletal_muscle 0 .00 RPM 168 .11 RPM
bodymap2_testis 0 .06 RPM 132 .46 RPM
bodymap2_thyroid 0 .09 RPM 215 .64 RPM
bodymap2_white_blood_cells 0 .00 RPM 268 .25 RPM
RNA Polymerase II actvity may be related with retro_hsap_139 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CMI POLR2A 1:38010144..38010534
No EST(s) were mapped for retro_hsap_139 retrocopy.
No TSS is located nearby retro_hsap_139 retrocopy 5' end.
retro_hsap_139 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_139 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_479

Parental genes homology:
Parental genes homology involve 20 parental genes, and 255 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000168311 retrocopy
Canis familiaris ENSCAFG000000159011 retrocopy
Callithrix jacchus ENSCJAG0000001908916 retrocopies
Cavia porcellus ENSCPOG000000265863 retrocopies
Dasypus novemcinctus ENSDNOG0000001712883 retrocopies
Felis catus ENSFCAG000000073821 retrocopy
Homo sapiens ENSG0000008708611 retrocopies
Homo sapiens ENSG00000167996 20 retrocopies
Latimeria chalumnae ENSLACG000000174261 retrocopy
Loxodonta africana ENSLAFG0000000482412 retrocopies
Myotis lucifugus ENSMLUG0000002572616 retrocopies
Monodelphis domestica ENSMODG000000075829 retrocopies
Mus musculus ENSMUSG000000246614 retrocopies
Nomascus leucogenys ENSNLEG0000000332129 retrocopies
Oryctolagus cuniculus ENSOCUG000000141084 retrocopies
Procavia capensis ENSPCAG0000001037713 retrocopies
Pongo abelii ENSPPYG0000000317312 retrocopies
Rattus norvegicus ENSRNOG000000226199 retrocopies
Sus scrofa ENSSSCG000000145409 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000145211 retrocopy

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 = 0.23 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .23 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM


Indel association:

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




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