RetrogeneDB ID:

retro_hsap_4146

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:30935482..30935891(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000214020
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FTL
Ensembl ID:ENSG00000087086
Aliases:FTL, LFTD, NBIA3
Description:ferritin, light polypeptide [Source:HGNC Symbol;Acc:3999]


Retrocopy-Parental alignment summary:






>retro_hsap_4146
TATTCCACCAAGGTGGAAGCAGCCATCAACCACCTGATCAATTTGCATCTGCAGCCCTCCAGCACGTACCTTTCTCAGAA
CTTCTTTTCAACCATAACAATGTGCCTCTGGAAGGCATGGGCCACTTTATCTGTGAATTGACCAAGGAGAGGTGTGAGGG
TTCAGAACAACTCTTGAAGGTGCAAAACCAGCTTGGGGGCCATGCTCTCTTTCAGGATGTTCAGAAGCAATCTCAAAATG
AGTGGGGTAAAACCATGCATGTCTTGGAAGGTGCCATAGCCCTGGAGAAGGACATGAACCAGGACCTTTTGGATCTTCAT
GCACTGGGTTTGGCCACACAGATTTTCATCTCTGTGACTCCCTGGAGAGGCACTTTCTAGCTGAGGAAGTGAAACTCATC
AAGAAGATG

ORF - retro_hsap_4146 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.59 %
Parental protein coverage: 78.29 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalYSTDVEAAVNSLVNLYLQASYTYLSLGFY-FDRDDVALEGVSHFFRELAEEKREGYERLLKMQNQRGGRA
YST.VEAA.N.L.NL.LQ.S.TYLS..F..F....V.LEG..HF..EL..E..EG.E.LLK.QNQ.GG.A
RetrocopyYSTKVEAAINHLINLHLQPSSTYLSQNFF<FNHNNVPLEGMGHFICELTKERCEGSEQLLKVQNQLGGHA
ParentalLFQDIKKPAEDEWGKTPDAMKAAMALEKKLNQALLDLHALGSA-RTDPHLCDFLETHFLDEEVKLIKKM
LFQD..K....EWGKT......A.ALEK..NQ.LLDLHALG.A..TD.HLCD.LE.HFL.EEVKLIKKM
RetrocopyLFQDVQKQSQNEWGKTMHVLEGAIALEKDMNQDLLDLHALGLA<HTDFHLCDSLERHFLAEEVKLIKKM

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 1863 .91 RPM
bodymap2_adrenal 0 .00 RPM 1058 .95 RPM
bodymap2_brain 0 .00 RPM 272 .02 RPM
bodymap2_breast 0 .00 RPM 1738 .93 RPM
bodymap2_colon 0 .00 RPM 670 .92 RPM
bodymap2_heart 0 .00 RPM 243 .78 RPM
bodymap2_kidney 0 .00 RPM 1729 .69 RPM
bodymap2_liver 0 .00 RPM 2015 .73 RPM
bodymap2_lung 0 .00 RPM 2849 .70 RPM
bodymap2_lymph_node 0 .00 RPM 1616 .52 RPM
bodymap2_ovary 0 .00 RPM 779 .67 RPM
bodymap2_prostate 0 .00 RPM 1402 .23 RPM
bodymap2_skeletal_muscle 0 .00 RPM 372 .14 RPM
bodymap2_testis 0 .00 RPM 363 .05 RPM
bodymap2_thyroid 0 .00 RPM 908 .10 RPM
bodymap2_white_blood_cells 0 .00 RPM 1684 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4146 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4146 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4146 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4146 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4146 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2818
Gorilla gorilla retro_ggor_2784
Parental genes homology:
Parental genes homology involve 23 parental genes, and 309 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000001334333 retrocopies
retro_btau_1007, retro_btau_1011, retro_btau_1033, retro_btau_1197, retro_btau_1209, retro_btau_1277, retro_btau_1354, retro_btau_1396, retro_btau_1452, retro_btau_1464, retro_btau_1466, retro_btau_1481, retro_btau_1511, retro_btau_1540, retro_btau_1561, retro_btau_1683, retro_btau_1781, retro_btau_1798, retro_btau_1848, retro_btau_250, retro_btau_301, retro_btau_339, retro_btau_340, retro_btau_419, retro_btau_422, retro_btau_520, retro_btau_597, retro_btau_639, retro_btau_649, retro_btau_938, retro_btau_963, retro_btau_993, retro_btau_998,
Canis familiaris ENSCAFG000000038611 retrocopy
retro_cfam_203,
Callithrix jacchus ENSCJAG0000000025013 retrocopies
retro_cjac_1171, retro_cjac_1208, retro_cjac_1264, retro_cjac_1643, retro_cjac_2272, retro_cjac_2780, retro_cjac_3113, retro_cjac_3254, retro_cjac_3879, retro_cjac_556, retro_cjac_60, retro_cjac_889, retro_cjac_997,
Cavia porcellus ENSCPOG000000205581 retrocopy
retro_cpor_100,
Dasypus novemcinctus ENSDNOG000000024559 retrocopies
retro_dnov_1096, retro_dnov_1135, retro_dnov_1177, retro_dnov_1737, retro_dnov_2006, retro_dnov_2352, retro_dnov_2678, retro_dnov_473, retro_dnov_993,
Dasypus novemcinctus ENSDNOG000000041265 retrocopies
retro_dnov_1263, retro_dnov_1490, retro_dnov_1760, retro_dnov_2329, retro_dnov_299,
Dasypus novemcinctus ENSDNOG0000000557736 retrocopies
retro_dnov_103, retro_dnov_1164, retro_dnov_1215, retro_dnov_130, retro_dnov_1382, retro_dnov_1441, retro_dnov_1515, retro_dnov_1568, retro_dnov_1657, retro_dnov_1812, retro_dnov_1815, retro_dnov_1918, retro_dnov_1991, retro_dnov_2014, retro_dnov_2134, retro_dnov_2187, retro_dnov_236, retro_dnov_2376, retro_dnov_2379, retro_dnov_247, retro_dnov_2575, retro_dnov_2658, retro_dnov_2667, retro_dnov_285, retro_dnov_305, retro_dnov_432, retro_dnov_439, retro_dnov_543, retro_dnov_598, retro_dnov_642, retro_dnov_807, retro_dnov_841, retro_dnov_846, retro_dnov_849, retro_dnov_861, retro_dnov_897,
Dasypus novemcinctus ENSDNOG000000078482 retrocopies
retro_dnov_1049, retro_dnov_1476,
Dasypus novemcinctus ENSDNOG000000166838 retrocopies
retro_dnov_1134, retro_dnov_1329, retro_dnov_2023, retro_dnov_2194, retro_dnov_2228, retro_dnov_56, retro_dnov_757, retro_dnov_886,
Felis catus ENSFCAG0000000334837 retrocopies
retro_fcat_101, retro_fcat_1029, retro_fcat_1040, retro_fcat_1059, retro_fcat_1141, retro_fcat_1150, retro_fcat_1295, retro_fcat_1319, retro_fcat_1336, retro_fcat_1359, retro_fcat_139, retro_fcat_1522, retro_fcat_1523, retro_fcat_1602, retro_fcat_1658, retro_fcat_1741, retro_fcat_1747, retro_fcat_1764, retro_fcat_1765, retro_fcat_1766, retro_fcat_1799, retro_fcat_1812, retro_fcat_1901, retro_fcat_297, retro_fcat_298, retro_fcat_315, retro_fcat_343, retro_fcat_50, retro_fcat_533, retro_fcat_536, retro_fcat_620, retro_fcat_675, retro_fcat_68, retro_fcat_778, retro_fcat_918, retro_fcat_927, retro_fcat_964,
Homo sapiens ENSG00000087086 11 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 ENSG0000016799620 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,
Gorilla gorilla ENSGGOG000000119999 retrocopies
retro_ggor_128, retro_ggor_1547, retro_ggor_2039, retro_ggor_25, retro_ggor_2784, retro_ggor_2894, retro_ggor_420, retro_ggor_677, retro_ggor_750,
Loxodonta africana ENSLAFG0000003124811 retrocopies
retro_lafr_1003, retro_lafr_1064, retro_lafr_1065, retro_lafr_1069, retro_lafr_1206, retro_lafr_255, retro_lafr_345, retro_lafr_346, retro_lafr_785, retro_lafr_836, retro_lafr_977,
Macaca mulatta ENSMMUG000000039099 retrocopies
retro_mmul_1051, retro_mmul_1125, retro_mmul_1508, retro_mmul_1569, retro_mmul_1617, retro_mmul_1950, retro_mmul_481, retro_mmul_518, retro_mmul_989,
Mustela putorius furoENSMPUG0000000330429 retrocopies
retro_mputfur_1012, retro_mputfur_1026, retro_mputfur_1133, retro_mputfur_1142, retro_mputfur_1150, retro_mputfur_1216, retro_mputfur_1222, retro_mputfur_1225, retro_mputfur_1238, retro_mputfur_1246, retro_mputfur_1268, retro_mputfur_1303, retro_mputfur_1335, retro_mputfur_1521, retro_mputfur_1620, retro_mputfur_195, retro_mputfur_222, retro_mputfur_265, retro_mputfur_350, retro_mputfur_356, retro_mputfur_368, retro_mputfur_482, retro_mputfur_66, retro_mputfur_702, retro_mputfur_741, retro_mputfur_80, retro_mputfur_820, retro_mputfur_906, retro_mputfur_952,
Mus musculus ENSMUSG000000507081 retrocopy
retro_mmus_228,
Nomascus leucogenys ENSNLEG0000000471610 retrocopies
retro_nleu_1099, retro_nleu_1332, retro_nleu_1871, retro_nleu_1977, retro_nleu_2028, retro_nleu_2180, retro_nleu_2294, retro_nleu_2715, retro_nleu_272, retro_nleu_290,
Oryctolagus cuniculus ENSOCUG000000000146 retrocopies
retro_ocun_1090, retro_ocun_1627, retro_ocun_223, retro_ocun_357, retro_ocun_530, retro_ocun_982,
Pan troglodytes ENSPTRG0000001126811 retrocopies
retro_ptro_1118, retro_ptro_1307, retro_ptro_1437, retro_ptro_2055, retro_ptro_2619, retro_ptro_2818, retro_ptro_3101, retro_ptro_3195, retro_ptro_328, retro_ptro_645, retro_ptro_98,
Rattus norvegicus ENSRNOG000000208437 retrocopies
retro_rnor_109, retro_rnor_168, retro_rnor_263, retro_rnor_306, retro_rnor_362, retro_rnor_373, retro_rnor_4,
Sus scrofa ENSSSCG0000000315333 retrocopies
retro_sscr_1040, retro_sscr_1095, retro_sscr_1101, retro_sscr_1142, retro_sscr_1189, retro_sscr_1214, retro_sscr_1215, retro_sscr_124, retro_sscr_197, retro_sscr_212, retro_sscr_224, retro_sscr_305, retro_sscr_331, retro_sscr_400, retro_sscr_531, retro_sscr_532, retro_sscr_533, retro_sscr_534, retro_sscr_535, retro_sscr_536, retro_sscr_559, retro_sscr_589, retro_sscr_605, retro_sscr_74, retro_sscr_747, retro_sscr_799, retro_sscr_817, retro_sscr_830, retro_sscr_833, retro_sscr_839, retro_sscr_840, retro_sscr_862, retro_sscr_898,
Ictidomys tridecemlineatus ENSSTOG000000206397 retrocopies
retro_itri_1606, retro_itri_1701, retro_itri_1857, retro_itri_24, retro_itri_355, retro_itri_719, retro_itri_741,

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 = 0.02 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 .02 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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