RetrogeneDB ID: retro_hsap_1204

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:52034778..52035429(+)
• Located in intron of: ENSG00000236778

Retrocopy information

• Ensembl ID: ENSG00000224892
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS4X
• Ensembl ID: ENSG00000198034
• Aliases: None
• Description: ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]

Sequence

>retro_hsap_1204
GAGTGTCTTCCCCTCATCATTTTCCTAAGGAACAGACTTAAGTATGCCCTGGAAGGAGATGAAGTAAAGAAGATTTGCAT
GCAGCGGTTTATTAAAATTGATGGCAAGGTCTAAACTGATATAACCTACCCTGCTGGATTCATGGAGGCCATCAGCATTG
ACAAGACAGAAGAGAATTTCTCTCTGATCTATGACACCAAGAGTCTCTTTGCTGTACATCATATTACACCTGAGGAGGCC
AAGTACAAGTTGTGCAAAGTGAGAAAAATCTTTCTGGGAACAAAAGGAATCCCTCATCTGGTGACTCATGATGGTCGCAC
CATCCGCTACACTGATCCCCTTATCAAGGTGAATGATACCATTCAGATTGATTTGGAGACTGGCAAGATTACTGATTTCA
TCAAATTCGACACTGGTCACCTGTGTATGGTGACTGGAGGTGCTAACCTGGGAAGAATTGGTGTGATCACCAACAGAGAG
AGGCACCCTGGATCTTTTGACATTGTTCACATGGAAGATGCCAATGGCAACAGCTTTGCCACTCAACTTTCCAACATTTT
TGTTATTGGCAAGGGCAACAAACTATGGATTTCTCTTCCCTGAGGAAAGGGTATCCGCCTCACCATTGCTGAAGAGAGAG
ACAAAAGACTG

Alignment

ORF - retro_hsap_1204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.24 %
• Parental protein coverage: 82.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRF
          ECLPLIIFLRNRLKYAL.GDEVKKICMQRFIKIDGKV.TDITYPAGFM..ISIDKT.ENF.LIYDTK..F
Retrocopy ECLPLIIFLRNRLKYALEGDEVKKICMQRFIKIDGKV*TDITYPAGFMEAISIDKTEENFSLIYDTKSLF

Parental  AVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGN
          AVH.ITPEEAKYKLCKVRKIF.GTKGIPHLVTHD.RTIRY.DPLIKVNDTIQIDLETGKITDFIKFDTG.
Retrocopy AVHHITPEEAKYKLCKVRKIFLGTKGIPHLVTHDGRTIRYTDPLIKVNDTIQIDLETGKITDFIKFDTGH

Parental  LCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIA
          LCMVTGGANLGRIGVITNRERHPGSFD.VH..DANGNSFAT.LSNIFVIGKGNK.WISLP.GKGIRLTIA
Retrocopy LCMVTGGANLGRIGVITNRERHPGSFDIVHMEDANGNSFATQLSNIFVIGKGNKLWISLP*GKGIRLTIA

Parental  EERDKRL
          EERDKRL
Retrocopy EERDKRL

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	0.18 RPM	1077.78 RPM
bodymap2_adrenal	0.47 RPM	994.39 RPM
bodymap2_brain	0.02 RPM	249.47 RPM
bodymap2_breast	0.19 RPM	912.87 RPM
bodymap2_colon	0.23 RPM	1472.93 RPM
bodymap2_heart	0.37 RPM	215.90 RPM
bodymap2_kidney	0.41 RPM	575.10 RPM
bodymap2_liver	0.15 RPM	226.26 RPM
bodymap2_lung	0.30 RPM	826.90 RPM
bodymap2_lymph_node	2.67 RPM	1412.13 RPM
bodymap2_ovary	0.44 RPM	2009.69 RPM
bodymap2_prostate	1.14 RPM	1321.94 RPM
bodymap2_skeletal_muscle	1.25 RPM	719.78 RPM
bodymap2_testis	1.06 RPM	641.02 RPM
bodymap2_thyroid	0.38 RPM	887.86 RPM
bodymap2_white_blood_cells	0.85 RPM	1229.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1204 was not detected

EST

No EST(s) were mapped for retro_hsap_1204 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_33800	111 libraries	66 libraries	722 libraries	645 libraries	285 libraries

The graphical summary, for retro_hsap_1204 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_1204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1204 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_939
Pongo abelii	retro_pabe_1005

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 210 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Bos taurus	ENSBTAG00000018800	5 retrocopies	retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris	ENSCAFG00000017151	2 retrocopies	retro_cfam_165, retro_cfam_194,
Callithrix jacchus	ENSCJAG00000004192	2 retrocopies	retro_cjac_19, retro_cjac_361,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Homo sapiens	ENSG00000198034	19 retrocopies	retro_hsap_1070, retro_hsap_1151, retro_hsap_120, retro_hsap_1204 , retro_hsap_1792, retro_hsap_1868, retro_hsap_2026, retro_hsap_2051, retro_hsap_2052, retro_hsap_2270, retro_hsap_2437, retro_hsap_2443, retro_hsap_3162, retro_hsap_3423, retro_hsap_3519, retro_hsap_3986, retro_hsap_4051, retro_hsap_656, retro_hsap_875,
Macropus eugenii	ENSMEUG00000007969	16 retrocopies	retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Microcebus murinus	ENSMICG00000016606	58 retrocopies	retro_mmur_1107, retro_mmur_1108, retro_mmur_1123, retro_mmur_1136, retro_mmur_1168, retro_mmur_1208, retro_mmur_1209, retro_mmur_1229, retro_mmur_1231, retro_mmur_1257, retro_mmur_1268, retro_mmur_1334, retro_mmur_1411, retro_mmur_1416, retro_mmur_1430, retro_mmur_1442, retro_mmur_1454, retro_mmur_1467, retro_mmur_1471, retro_mmur_1519, retro_mmur_1578, retro_mmur_1584, retro_mmur_1599, retro_mmur_1600, retro_mmur_1611, retro_mmur_166, retro_mmur_241, retro_mmur_281, retro_mmur_289, retro_mmur_293, retro_mmur_347, retro_mmur_363, retro_mmur_390, retro_mmur_510, retro_mmur_511, retro_mmur_521, retro_mmur_523, retro_mmur_530, retro_mmur_54, retro_mmur_551, retro_mmur_591, retro_mmur_609, retro_mmur_619, retro_mmur_663, retro_mmur_665, retro_mmur_687, retro_mmur_767, retro_mmur_784, retro_mmur_828, retro_mmur_840, retro_mmur_917, retro_mmur_918, retro_mmur_931, retro_mmur_943, retro_mmur_946, retro_mmur_949, retro_mmur_96, retro_mmur_995,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus	ENSMUSG00000031320	13 retrocopies	retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Nomascus leucogenys	ENSNLEG00000018121	25 retrocopies	retro_nleu_1127, retro_nleu_1226, retro_nleu_1361, retro_nleu_142, retro_nleu_1442, retro_nleu_1907, retro_nleu_1908, retro_nleu_2089, retro_nleu_2256, retro_nleu_244, retro_nleu_2461, retro_nleu_2495, retro_nleu_2587, retro_nleu_2613, retro_nleu_2640, retro_nleu_2646, retro_nleu_2776, retro_nleu_2801, retro_nleu_2932, retro_nleu_2967, retro_nleu_2968, retro_nleu_486, retro_nleu_500, retro_nleu_560, retro_nleu_947,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Pongo abelii	ENSPPYG00000020462	24 retrocopies	retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586, retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325, retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes	ENSPTRG00000022025	9 retrocopies	retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Sus scrofa	ENSSSCG00000012405	5 retrocopies	retro_sscr_1070, retro_sscr_563, retro_sscr_580, retro_sscr_665, retro_sscr_973,
Vicugna pacos	ENSVPAG00000010952	4 retrocopies	retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.56 RPM
CEU_NA11843	1.02 RPM
CEU_NA11930	0.75 RPM
CEU_NA12004	0.38 RPM
CEU_NA12400	1.12 RPM
CEU_NA12751	0.97 RPM
CEU_NA12760	0.49 RPM
CEU_NA12827	0.71 RPM
CEU_NA12872	0.33 RPM
CEU_NA12873	0.83 RPM
FIN_HG00183	1.24 RPM
FIN_HG00277	1.22 RPM
FIN_HG00315	0.91 RPM
FIN_HG00321	0.73 RPM
FIN_HG00328	0.40 RPM
FIN_HG00338	0.66 RPM
FIN_HG00349	0.46 RPM
FIN_HG00375	0.90 RPM
FIN_HG00377	0.40 RPM
FIN_HG00378	0.51 RPM
GBR_HG00099	0.55 RPM
GBR_HG00111	0.47 RPM
GBR_HG00114	0.63 RPM
GBR_HG00119	1.44 RPM
GBR_HG00131	1.03 RPM
GBR_HG00133	0.80 RPM
GBR_HG00134	1.03 RPM
GBR_HG00137	0.71 RPM
GBR_HG00142	1.69 RPM
GBR_HG00143	0.51 RPM
TSI_NA20512	0.34 RPM
TSI_NA20513	0.77 RPM
TSI_NA20518	0.50 RPM
TSI_NA20532	0.99 RPM
TSI_NA20538	0.97 RPM
TSI_NA20756	0.49 RPM
TSI_NA20765	0.89 RPM
TSI_NA20771	0.65 RPM
TSI_NA20786	0.26 RPM
TSI_NA20798	0.72 RPM
YRI_NA18870	1.02 RPM
YRI_NA18907	0.35 RPM
YRI_NA18916	1.05 RPM
YRI_NA19093	0.55 RPM
YRI_NA19099	0.83 RPM
YRI_NA19114	0.71 RPM
YRI_NA19118	0.68 RPM
YRI_NA19213	0.88 RPM
YRI_NA19214	0.42 RPM
YRI_NA19223	0.84 RPM

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Indel association:

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