RetrogeneDB ID:

retro_hsap_4671

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:37364586..37365116(+)
Located in intron of:ENSG00000250349
Retrocopy
information
Ensembl ID:ENSG00000234355
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_4671
TCGCAGGTGCACCAGAACAACCATCTCAGCTGCGAGGTCGCCATCAACATCAAGGTCACCCTGGAGCTCCACGCCTCCTA
TGTGTACCTGTCCATGGCCTTCTTCTTCGACCGGGACGACGTGGCCCTGGAGAGCTTCAGCCGCTATTTCTTGCACCAGT
GGCACGAGAAGAGGGAGCACGCCCAGGAGCTGATGAGCCTGCAGAACCTGCGCGGTGGCCGCATCTACCTTCGCGACATC
AGGAAGCCAGAGTGCCAAGGCTGGGAGAGCGGGCTCCAGGCCATGGACTGCGCCTTCTACCTGGAGAAGAACGTCAACCA
GAGCCTCCTGGAGCTGCACCAGCTGGCCAAGGAGAACGACGACCCCACCTCTGTGACTTCCTGGAGAACCACTTCCTGAA
CCAGCAGGCCAAGACCATCAAAGAGATTGGTGGCTACCTGAGCAACCTGTGCAAGATGGGGGCCCCGGAAGCAGGCCTGG
CAGAGTACCTCTTTAACAAGCTCACCCTGGGCCGCAGCCAGAAACACACC

ORF - retro_hsap_4671 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.29 %
Parental protein coverage: 96.72 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQ
SQV.QN.H...E.AIN....LEL.ASYVYLSM...FDRDDVAL..F..YFLHQ.HE.REHA..LM.LQN.
RetrocopySQVHQNNHLSCEVAINIKVTLELHASYVYLSMAFFFDRDDVALESFSRYFLHQWHEKREHAQELMSLQNL
ParentalRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKND-PHLCDFIETHYLNEQVKA
RGGRI.L.DI.KP.C..WESGL.AM.CA..LEKNVNQSLLELH.LA....D.PHLCDF.E.H.LN.Q.K.
RetrocopyRGGRIYLRDIRKPECQGWESGLQAMDCAFYLEKNVNQSLLELHQLAKENDD<PHLCDFLENHFLNQQAKT
ParentalIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSDNES
IKE.G....NL.KMGAPE.GLAEYLF.K.TLG.S....
RetrocopyIKEIGGYLSNLCKMGAPEAGLAEYLFNKLTLGRSQKHT

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 416 .48 RPM
bodymap2_adrenal 0 .00 RPM 130 .06 RPM
bodymap2_brain 0 .00 RPM 173 .50 RPM
bodymap2_breast 0 .00 RPM 294 .30 RPM
bodymap2_colon 0 .00 RPM 231 .41 RPM
bodymap2_heart 0 .00 RPM 98 .19 RPM
bodymap2_kidney 0 .00 RPM 318 .29 RPM
bodymap2_liver 0 .00 RPM 82 .81 RPM
bodymap2_lung 0 .00 RPM 442 .70 RPM
bodymap2_lymph_node 0 .07 RPM 156 .57 RPM
bodymap2_ovary 0 .00 RPM 138 .99 RPM
bodymap2_prostate 0 .00 RPM 201 .36 RPM
bodymap2_skeletal_muscle 0 .00 RPM 168 .11 RPM
bodymap2_testis 0 .00 RPM 132 .46 RPM
bodymap2_thyroid 0 .00 RPM 215 .64 RPM
bodymap2_white_blood_cells 0 .00 RPM 268 .25 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4671 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4671 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4671 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4671 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4671 has 0 orthologous retrocopies within eutheria group .

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

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000168311 retrocopy
retro_amel_115,
Canis familiaris ENSCAFG000000159011 retrocopy
retro_cfam_150,
Callithrix jacchus ENSCJAG0000001908916 retrocopies
retro_cjac_1570, retro_cjac_1634, retro_cjac_2115, retro_cjac_2233, retro_cjac_230, retro_cjac_232, retro_cjac_2320, retro_cjac_2531, retro_cjac_278, retro_cjac_2843, retro_cjac_2857, retro_cjac_485, retro_cjac_519, retro_cjac_699, retro_cjac_767, retro_cjac_804,
Cavia porcellus ENSCPOG000000265863 retrocopies
retro_cpor_1309, retro_cpor_15, retro_cpor_157,
Dasypus novemcinctus ENSDNOG0000001712883 retrocopies
retro_dnov_1017, retro_dnov_1074, retro_dnov_1078, retro_dnov_110, retro_dnov_1179, retro_dnov_1188, retro_dnov_1196, retro_dnov_1201, retro_dnov_1205, retro_dnov_1271, retro_dnov_1352, retro_dnov_1356, retro_dnov_1369, retro_dnov_1397, retro_dnov_1415, retro_dnov_1425, retro_dnov_1446, retro_dnov_1489, retro_dnov_1526, retro_dnov_1535, retro_dnov_1554, retro_dnov_1565, retro_dnov_162, retro_dnov_1627, retro_dnov_1640, retro_dnov_1777, retro_dnov_1787, retro_dnov_1792, retro_dnov_1827, retro_dnov_1851, retro_dnov_1865, retro_dnov_1875, retro_dnov_189, retro_dnov_197, retro_dnov_2005, retro_dnov_2065, retro_dnov_2093, retro_dnov_2097, retro_dnov_2109, retro_dnov_2124, retro_dnov_2136, retro_dnov_2154, retro_dnov_2173, retro_dnov_220, retro_dnov_2216, retro_dnov_2231, retro_dnov_2241, retro_dnov_2251, retro_dnov_2356, retro_dnov_2388, retro_dnov_2399, retro_dnov_242, retro_dnov_2443, retro_dnov_2444, retro_dnov_2454, retro_dnov_2476, retro_dnov_2483, retro_dnov_2489, retro_dnov_2511, retro_dnov_2528, retro_dnov_2554, retro_dnov_2579, retro_dnov_2607, retro_dnov_2626, retro_dnov_2646, retro_dnov_304, retro_dnov_383, retro_dnov_409, retro_dnov_422, retro_dnov_471, retro_dnov_517, retro_dnov_52, retro_dnov_55, retro_dnov_589, retro_dnov_61, retro_dnov_661, retro_dnov_675, retro_dnov_722, retro_dnov_726, retro_dnov_810, retro_dnov_864, retro_dnov_890, retro_dnov_994,
Felis catus ENSFCAG000000073821 retrocopy
retro_fcat_887,
Homo sapiens ENSG0000008708611 retrocopies
retro_hsap_1647, retro_hsap_1955, retro_hsap_2407, retro_hsap_2484, retro_hsap_2942, retro_hsap_3842, retro_hsap_4146, retro_hsap_431, retro_hsap_4665, retro_hsap_4805, retro_hsap_929,
Homo sapiens ENSG00000167996 20 retrocopies
retro_hsap_1243, retro_hsap_139, retro_hsap_1432, retro_hsap_2240, retro_hsap_2351, retro_hsap_2662, retro_hsap_2835, retro_hsap_2985, retro_hsap_2996, retro_hsap_316, retro_hsap_3208, retro_hsap_3293, retro_hsap_3589, retro_hsap_4083, retro_hsap_4232, retro_hsap_4671 , retro_hsap_484, retro_hsap_81, retro_hsap_87, retro_hsap_898,
Latimeria chalumnae ENSLACG000000174261 retrocopy
retro_lcha_75,
Loxodonta africana ENSLAFG0000000482412 retrocopies
retro_lafr_106, retro_lafr_1080, retro_lafr_1129, retro_lafr_138, retro_lafr_321, retro_lafr_433, retro_lafr_523, retro_lafr_53, retro_lafr_624, retro_lafr_717, retro_lafr_760, retro_lafr_966,
Myotis lucifugus ENSMLUG0000002572616 retrocopies
retro_mluc_1030, retro_mluc_1142, retro_mluc_1211, retro_mluc_1354, retro_mluc_1464, retro_mluc_1769, retro_mluc_1984, retro_mluc_2002, retro_mluc_2091, retro_mluc_212, retro_mluc_2635, retro_mluc_361, retro_mluc_532, retro_mluc_556, retro_mluc_850, retro_mluc_885,
Monodelphis domestica ENSMODG000000075829 retrocopies
retro_mdom_1134, retro_mdom_122, retro_mdom_1294, retro_mdom_1407, retro_mdom_1742, retro_mdom_300, retro_mdom_564, retro_mdom_643, retro_mdom_809,
Mus musculus ENSMUSG000000246614 retrocopies
retro_mmus_2856, retro_mmus_3417, retro_mmus_3660, retro_mmus_45,
Nomascus leucogenys ENSNLEG0000000332129 retrocopies
retro_nleu_1036, retro_nleu_1157, retro_nleu_136, retro_nleu_1411, retro_nleu_1503, retro_nleu_1532, retro_nleu_1732, retro_nleu_1886, retro_nleu_2049, retro_nleu_2143, retro_nleu_2162, retro_nleu_2163, retro_nleu_2281, retro_nleu_2356, retro_nleu_2357, retro_nleu_2358, retro_nleu_2359, retro_nleu_2360, retro_nleu_2361, retro_nleu_2417, retro_nleu_2433, retro_nleu_2962, retro_nleu_303, retro_nleu_383, retro_nleu_72, retro_nleu_738, retro_nleu_747, retro_nleu_78, retro_nleu_936,
Oryctolagus cuniculus ENSOCUG000000141084 retrocopies
retro_ocun_1172, retro_ocun_1179, retro_ocun_1598, retro_ocun_93,
Procavia capensis ENSPCAG0000001037713 retrocopies
retro_pcap_177, retro_pcap_217, retro_pcap_248, retro_pcap_276, retro_pcap_344, retro_pcap_348, retro_pcap_374, retro_pcap_379, retro_pcap_383, retro_pcap_395, retro_pcap_447, retro_pcap_5, retro_pcap_62,
Pongo abelii ENSPPYG0000000317312 retrocopies
retro_pabe_1034, retro_pabe_1186, retro_pabe_2410, retro_pabe_2483, retro_pabe_2484, retro_pabe_249, retro_pabe_3351, retro_pabe_3406, retro_pabe_35, retro_pabe_3713, retro_pabe_47, retro_pabe_479,
Rattus norvegicus ENSRNOG000000226199 retrocopies
retro_rnor_1197, retro_rnor_1280, retro_rnor_1356, retro_rnor_1832, retro_rnor_2060, retro_rnor_2163, retro_rnor_264, retro_rnor_427, retro_rnor_71,
Sus scrofa ENSSSCG000000145409 retrocopies
retro_sscr_1045, retro_sscr_168, retro_sscr_286, retro_sscr_359, retro_sscr_498, retro_sscr_581, retro_sscr_78, retro_sscr_906, retro_sscr_949,
Ictidomys tridecemlineatus ENSSTOG000000145211 retrocopy
retro_itri_250,

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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