RetrogeneDB ID: retro_hsap_1281

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:77555309..77556051(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000233873
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL7
• Ensembl ID: ENSG00000147604
• Aliases: RPL7, L7, humL7-1
• Description: ribosomal protein L7 [Source:HGNC Symbol;Acc:10363]

Sequence

>retro_hsap_1281
ATGGAGAGTGTCAAAGAGAAGAAGAAAAAGTTTCCTGCTGTACCAGAAACCCTTAAGAAAAAGCGAAGAAATTTCACAGA
GCTGAAGATCAAATGCCTGAGAAAGAAGTTTGCCCAAAAGATGCTTCGAAAGGCAAGGAGGAAGCTTATCTATGAAAAAG
CGAAGCACTATCACAAGGAATATAGACAGATATACGGAACTTAAATTTGAATGGCAAGGATGGCAAGCAAAGCCGGCAAC
TTCTATGTACCTGCAGAACCCAAATTGGCATTTGTCATCAGGATCAGAGGTATCAGTGGTGTGAGCCCAAAGGTCCGAAA
GGTGTTGCAGCTTCTTCGCCTTCGTCAAATCTTCAGTGGAAACTTTGTGAAGCTTAACAAGGTTTCAATTAACATGCTGG
GGATTGTAGAACCATATATTGCAGGGGGTACCCAAATCTGAAGTCAGTAAATAAACTAATCTACAAGCGGGGTTATGGCA
AAATCAATAAGAAGCGAATTGCTTTGACAGATAACGCTTTGATTGCTCGAACGCTTGGTAAATATGGCATCATCTGCACG
GAAGATCTGATTCATGAGATCTATACTGTTGGAAAATGCTTCGAAGAAGCAAATAACTTCCTGTGGTCCTTCAAATTATC
TTCTCCATGAGGTGGAAAGAAGAAAAAGACCACCCATTTTGTAGAAGGTGGAGATGCTGGCAACAGGGAGGACCAGATCA
ACAGCTTATTAGAATAATGAAC

Alignment

ORF - retro_hsap_1281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIR
          ME.V.EKKK..PAVPETLKKKRRNF.ELKIK.LRKKFAQKMLRKARRKLIYEKAKHYHKEYRQ.Y.T.I.
Retrocopy MESVKEKKKKFPAVPETLKKKRRNFTELKIKCLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQIYGT*I*

Parental  MARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYI
          MARMA.KAGNFYVPAEPKLAFVIRIRGI.GVSPKVRKVLQLLRLRQIF.G.FVKLNK.SINML.IVEPYI
Retrocopy MARMASKAGNFYVPAEPKLAFVIRIRGISGVSPKVRKVLQLLRLRQIFSGNFVKLNKVSINMLGIVEPYI

Parental  AW-GYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLW
          A..GYPNLKSVN.LIYKRGYGKINKKRIALTDNALIAR.LGKYGIIC.EDLIHEIYTVGK.F.EANNFLW
Retrocopy AG<GYPNLKSVNKLIYKRGYGKINKKRIALTDNALIARTLGKYGIICTEDLIHEIYTVGKCFEEANNFLW

Parental  PFKLSSPRGGMKKKTTHFVEGGDAGNREDQIN-RLIRRMN
          .FKLSSP.GG.KKKTTHFVEGGDAGNREDQIN..LIR.MN
Retrocopy SFKLSSP*GGKKKKTTHFVEGGDAGNREDQIN<QLIRIMN

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	0.04 RPM	732.70 RPM
bodymap2_adrenal	0.00 RPM	756.47 RPM
bodymap2_brain	0.00 RPM	227.86 RPM
bodymap2_breast	0.00 RPM	671.02 RPM
bodymap2_colon	0.02 RPM	1010.05 RPM
bodymap2_heart	0.00 RPM	163.75 RPM
bodymap2_kidney	0.00 RPM	459.62 RPM
bodymap2_liver	0.00 RPM	197.70 RPM
bodymap2_lung	0.00 RPM	567.88 RPM
bodymap2_lymph_node	0.00 RPM	697.27 RPM
bodymap2_ovary	0.02 RPM	1313.51 RPM
bodymap2_prostate	0.00 RPM	945.68 RPM
bodymap2_skeletal_muscle	0.00 RPM	360.36 RPM
bodymap2_testis	0.00 RPM	532.58 RPM
bodymap2_thyroid	0.00 RPM	532.91 RPM
bodymap2_white_blood_cells	0.00 RPM	845.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1281 was not detected

EST

No EST(s) were mapped for retro_hsap_1281 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_34393	178 libraries	85 libraries	879 libraries	538 libraries	149 libraries

The graphical summary, for retro_hsap_1281 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_1281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1281 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1061

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 257 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020139	22 retrocopies	retro_btau_1088, retro_btau_1231, retro_btau_1367, retro_btau_1381, retro_btau_1422, retro_btau_1434, retro_btau_1468, retro_btau_1548, retro_btau_1559, retro_btau_1616, retro_btau_1627, retro_btau_1784, retro_btau_1814, retro_btau_304, retro_btau_426, retro_btau_622, retro_btau_668, retro_btau_730, retro_btau_750, retro_btau_758, retro_btau_863, retro_btau_879,
Callithrix jacchus	ENSCJAG00000007686	1 retrocopy	retro_cjac_105,
Equus caballus	ENSECAG00000009188	1 retrocopy	retro_ecab_35,
Homo sapiens	ENSG00000146223	22 retrocopies	retro_hsap_1285, retro_hsap_1291, retro_hsap_1602, retro_hsap_1623, retro_hsap_1661, retro_hsap_1836, retro_hsap_2201, retro_hsap_2389, retro_hsap_2735, retro_hsap_2845, retro_hsap_3053, retro_hsap_3068, retro_hsap_3077, retro_hsap_3187, retro_hsap_3250, retro_hsap_3373, retro_hsap_3556, retro_hsap_3641, retro_hsap_3846, retro_hsap_3957, retro_hsap_4770, retro_hsap_4827,
Homo sapiens	ENSG00000147604	49 retrocopies	retro_hsap_1001, retro_hsap_1023, retro_hsap_1033, retro_hsap_1034, retro_hsap_1128, retro_hsap_113, retro_hsap_1232, retro_hsap_1281 , retro_hsap_1614, retro_hsap_1626, retro_hsap_1844, retro_hsap_1862, retro_hsap_1957, retro_hsap_2008, retro_hsap_203, retro_hsap_2093, retro_hsap_2101, retro_hsap_2588, retro_hsap_2837, retro_hsap_3197, retro_hsap_3204, retro_hsap_3244, retro_hsap_3254, retro_hsap_3356, retro_hsap_3399, retro_hsap_344, retro_hsap_3453, retro_hsap_3493, retro_hsap_3560, retro_hsap_3573, retro_hsap_3625, retro_hsap_3717, retro_hsap_3775, retro_hsap_3883, retro_hsap_3918, retro_hsap_4137, retro_hsap_415, retro_hsap_426, retro_hsap_4306, retro_hsap_4662, retro_hsap_4704, retro_hsap_4718, retro_hsap_4761, retro_hsap_558, retro_hsap_616, retro_hsap_708, retro_hsap_729, retro_hsap_973, retro_hsap_976,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Microcebus murinus	ENSMICG00000002880	8 retrocopies	retro_mmur_1170, retro_mmur_1379, retro_mmur_139, retro_mmur_158, retro_mmur_52, retro_mmur_596, retro_mmur_646, retro_mmur_903,
Macaca mulatta	ENSMMUG00000005141	1 retrocopy	retro_mmul_129,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Otolemur garnettii	ENSOGAG00000003903	2 retrocopies	retro_ogar_15, retro_ogar_225,
Pongo abelii	ENSPPYG00000018671	50 retrocopies	retro_pabe_1025, retro_pabe_1061, retro_pabe_1087, retro_pabe_1326, retro_pabe_1454, retro_pabe_1520, retro_pabe_1642, retro_pabe_1677, retro_pabe_1908, retro_pabe_1998, retro_pabe_2004, retro_pabe_2118, retro_pabe_2197, retro_pabe_2348, retro_pabe_2656, retro_pabe_2690, retro_pabe_2762, retro_pabe_2796, retro_pabe_2807, retro_pabe_2808, retro_pabe_2856, retro_pabe_2886, retro_pabe_2936, retro_pabe_2946, retro_pabe_307, retro_pabe_3085, retro_pabe_3117, retro_pabe_3139, retro_pabe_3191, retro_pabe_3414, retro_pabe_3468, retro_pabe_3506, retro_pabe_352, retro_pabe_3622, retro_pabe_3651, retro_pabe_3662, retro_pabe_3669, retro_pabe_3675, retro_pabe_436, retro_pabe_497, retro_pabe_514, retro_pabe_551, retro_pabe_628, retro_pabe_655, retro_pabe_826, retro_pabe_844, retro_pabe_859, retro_pabe_865, retro_pabe_867, retro_pabe_933,
Rattus norvegicus	ENSRNOG00000006992	27 retrocopies	retro_rnor_1018, retro_rnor_1174, retro_rnor_1222, retro_rnor_1233, retro_rnor_1307, retro_rnor_1388, retro_rnor_1466, retro_rnor_1580, retro_rnor_1745, retro_rnor_1916, retro_rnor_1944, retro_rnor_2025, retro_rnor_2028, retro_rnor_2100, retro_rnor_2247, retro_rnor_2304, retro_rnor_2347, retro_rnor_2531, retro_rnor_2715, retro_rnor_2765, retro_rnor_2814, retro_rnor_2824, retro_rnor_530, retro_rnor_666, retro_rnor_911, retro_rnor_929, retro_rnor_977,
Ictidomys tridecemlineatus	ENSSTOG00000004586	18 retrocopies	retro_itri_1025, retro_itri_1080, retro_itri_1358, retro_itri_1375, retro_itri_1412, retro_itri_1430, retro_itri_1464, retro_itri_1593, retro_itri_1776, retro_itri_271, retro_itri_346, retro_itri_349, retro_itri_351, retro_itri_390, retro_itri_534, retro_itri_542, retro_itri_827, retro_itri_917,
Tupaia belangeri	ENSTBEG00000002301	1 retrocopy	retro_tbel_2042,
Tarsius syrichta	ENSTSYG00000006100	25 retrocopies	retro_tsyr_1149, retro_tsyr_1200, retro_tsyr_1293, retro_tsyr_1297, retro_tsyr_1403, retro_tsyr_1598, retro_tsyr_1633, retro_tsyr_1850, retro_tsyr_1891, retro_tsyr_191, retro_tsyr_2109, retro_tsyr_2130, retro_tsyr_344, retro_tsyr_421, retro_tsyr_433, retro_tsyr_521, retro_tsyr_589, retro_tsyr_601, retro_tsyr_651, retro_tsyr_724, retro_tsyr_779, retro_tsyr_877, retro_tsyr_930, retro_tsyr_953, retro_tsyr_992,
Tursiops truncatus	ENSTTRG00000009074	16 retrocopies	retro_ttru_1241, retro_ttru_1546, retro_ttru_1690, retro_ttru_174, retro_ttru_1776, retro_ttru_1918, retro_ttru_210, retro_ttru_290, retro_ttru_367, retro_ttru_402, retro_ttru_534, retro_ttru_604, retro_ttru_726, retro_ttru_852, retro_ttru_933, retro_ttru_952,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.23 RPM
CEU_NA12400	0.18 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.15 RPM
FIN_HG00328	0.12 RPM
FIN_HG00338	0.15 RPM
FIN_HG00349	0.26 RPM
FIN_HG00375	0.20 RPM
FIN_HG00377	0.18 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.16 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.10 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.17 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.12 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.20 RPM
TSI_NA20786	0.08 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.08 RPM
YRI_NA19118	0.19 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.20 RPM
YRI_NA19223	0.14 RPM

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Indel association:

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