RetrogeneDB ID: retro_hsap_3293

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:17353984..17354532(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000223361
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• 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]

Sequence

>retro_hsap_3293
ATGACGACCGCGTCCACCTCACAGGTGCGCCAGGACTACCACCAGGACTAAAGGCCGCCATCAACCGCCAGATCAACCTG
GAGCTCTACGCCTCCTGCGTTTACCTGTCCATGTCTTACTACTTTGACCGCGATGATGTGGCTTTGAAGAACTTTGCCAA
ATACTTTCTTCACCAATCTCATGAGGAGAGGGAACATGCTGAGAAACTGATGAAGCTGCAGAACCAAGGAGGTGGCCGAA
TCTTCCTTCAGGATATCAAGAAACCGGACTGTGATGACTGGGAGAGCGGGCTGAATGCGATGGAGTGTGCATTACATTTG
GAAAAAAATGTGAATCAGTCACTACTGGAACTGCACAAACTGGCCACTGACAAAAATGACCCCCATTTGTGTGACTTCAT
TGAGACACATTACCTGAATGAGCAGGTCAAAGCCATCAAAGAATTGGGTGACCACATGACCAACTTGTGCAAGATGGGAG
CACCCGAATCTAGCTTGGCGGAATATCTCTTTGACCAGCACACCCTGGGAGACAGTGATAATGAAAGC

Alignment

ORF - retro_hsap_3293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTASTSQVRQNYHQD-SEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEK
          MTTASTSQVRQ.YHQD...AAINRQINLELYAS.VYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEK
Retrocopy MTTASTSQVRQDYHQD<LKAAINRQINLELYASCVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEK

Parental  LMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYL
          LMKLQNQ.GGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYL
Retrocopy LMKLQNQGGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYL

Parental  NEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSDNES
          NEQVKAIKELGDH.TNL.KMGAPES.LAEYLFD.HTLGDSDNES
Retrocopy NEQVKAIKELGDHMTNLCKMGAPESSLAEYLFDQHTLGDSDNES

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.46 RPM	416.48 RPM
bodymap2_adrenal	0.20 RPM	130.06 RPM
bodymap2_brain	0.09 RPM	173.50 RPM
bodymap2_breast	0.39 RPM	294.30 RPM
bodymap2_colon	0.15 RPM	231.41 RPM
bodymap2_heart	0.26 RPM	98.19 RPM
bodymap2_kidney	0.08 RPM	318.29 RPM
bodymap2_liver	0.04 RPM	82.81 RPM
bodymap2_lung	0.07 RPM	442.70 RPM
bodymap2_lymph_node	0.07 RPM	156.57 RPM
bodymap2_ovary	0.15 RPM	138.99 RPM
bodymap2_prostate	0.26 RPM	201.36 RPM
bodymap2_skeletal_muscle	0.84 RPM	168.11 RPM
bodymap2_testis	0.57 RPM	132.46 RPM
bodymap2_thyroid	0.28 RPM	215.64 RPM
bodymap2_white_blood_cells	0.26 RPM	268.25 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3293 was not detected

EST

No EST(s) were mapped for retro_hsap_3293 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_152473	152 libraries	259 libraries	812 libraries	245 libraries	361 libraries

The graphical summary, for retro_hsap_3293 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_3293 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3293 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1313

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016831	1 retrocopy	retro_amel_115,
Canis familiaris	ENSCAFG00000015901	1 retrocopy	retro_cfam_150,
Callithrix jacchus	ENSCJAG00000019089	16 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	ENSCPOG00000026586	3 retrocopies	retro_cpor_1309, retro_cpor_15, retro_cpor_157,
Dasypus novemcinctus	ENSDNOG00000017128	83 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	ENSFCAG00000007382	1 retrocopy	retro_fcat_887,
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	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	ENSLACG00000017426	1 retrocopy	retro_lcha_75,
Loxodonta africana	ENSLAFG00000004824	12 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	ENSMLUG00000025726	16 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	ENSMODG00000007582	9 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	ENSMUSG00000024661	4 retrocopies	retro_mmus_2856, retro_mmus_3417, retro_mmus_3660, retro_mmus_45,
Nomascus leucogenys	ENSNLEG00000003321	29 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	ENSOCUG00000014108	4 retrocopies	retro_ocun_1172, retro_ocun_1179, retro_ocun_1598, retro_ocun_93,
Procavia capensis	ENSPCAG00000010377	13 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	ENSPPYG00000003173	12 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	ENSRNOG00000022619	9 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	ENSSSCG00000014540	9 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	ENSSTOG00000014521	1 retrocopy	retro_itri_250,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.26 RPM
CEU_NA11843	0.37 RPM
CEU_NA11930	0.72 RPM
CEU_NA12004	0.19 RPM
CEU_NA12400	0.35 RPM
CEU_NA12751	0.15 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.33 RPM
CEU_NA12872	0.33 RPM
CEU_NA12873	0.38 RPM
FIN_HG00183	0.52 RPM
FIN_HG00277	0.26 RPM
FIN_HG00315	0.19 RPM
FIN_HG00321	0.12 RPM
FIN_HG00328	0.38 RPM
FIN_HG00338	0.19 RPM
FIN_HG00349	0.94 RPM
FIN_HG00375	0.44 RPM
FIN_HG00377	0.28 RPM
FIN_HG00378	0.34 RPM
GBR_HG00099	0.35 RPM
GBR_HG00111	0.30 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.29 RPM
GBR_HG00131	0.29 RPM
GBR_HG00133	0.22 RPM
GBR_HG00134	0.33 RPM
GBR_HG00137	0.33 RPM
GBR_HG00142	0.44 RPM
GBR_HG00143	0.19 RPM
TSI_NA20512	0.37 RPM
TSI_NA20513	0.39 RPM
TSI_NA20518	0.42 RPM
TSI_NA20532	0.51 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.70 RPM
TSI_NA20765	0.21 RPM
TSI_NA20771	0.34 RPM
TSI_NA20786	0.37 RPM
TSI_NA20798	0.31 RPM
YRI_NA18870	0.24 RPM
YRI_NA18907	0.24 RPM
YRI_NA18916	0.34 RPM
YRI_NA19093	0.26 RPM
YRI_NA19099	0.43 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.27 RPM
YRI_NA19213	0.69 RPM
YRI_NA19214	0.17 RPM
YRI_NA19223	0.20 RPM

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Indel association:

The presence of retro_hsap_3293 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_3293 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	5:17342773..17357200	99.18	100	100	100	100	99.17	100	100	97.19	100	100	100	100	100

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Indel #1, located at the genomic coordinates 5:17342773..17357200.