RetrogeneDB ID: retro_hsap_769

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:32779813..32780017(+)
• Located in intron of: ENSG00000186714

Retrocopy information

• Ensembl ID: ENSG00000244535
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSG00000109475
• Aliases: RPL34, L34
• Description: ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]

Sequence

>retro_hsap_769
ATGGTCCAGCATTTGACGTATCATCATGGGCTTTCCTACAATACAGCCTCTAACAAAACTAGGCTGTCCCAAACCCCTGG
TAATAGAATTGTTTACCTTTATACCAAGAAGGTTAGGAAAGCACCAAAATCTCCACGTGGCATGCCTCCAAGTAGATTTC
AAGGAGTTTGTGCTGTGAGACCTAAAGTTCTTATGAGGTTATCT

Alignment

ORF - retro_hsap_769 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.41 %
• Parental protein coverage: 58.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLS
          MVQ.LTY...LSYNTASNKTRLS.TPGNRIVYLYTKKV.KAPKS..G..P.R..GV.AVRPKVLMRLS
Retrocopy MVQHLTYHHGLSYNTASNKTRLSQTPGNRIVYLYTKKVRKAPKSPRGMPPSRFQGVCAVRPKVLMRLS

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	0.00 RPM	419.31 RPM
bodymap2_adrenal	0.00 RPM	769.57 RPM
bodymap2_brain	0.00 RPM	183.84 RPM
bodymap2_breast	0.00 RPM	451.46 RPM
bodymap2_colon	0.00 RPM	750.27 RPM
bodymap2_heart	0.00 RPM	148.09 RPM
bodymap2_kidney	0.00 RPM	272.59 RPM
bodymap2_liver	0.06 RPM	186.14 RPM
bodymap2_lung	0.14 RPM	692.23 RPM
bodymap2_lymph_node	0.00 RPM	808.72 RPM
bodymap2_ovary	0.00 RPM	610.59 RPM
bodymap2_prostate	0.00 RPM	887.12 RPM
bodymap2_skeletal_muscle	0.00 RPM	251.28 RPM
bodymap2_testis	0.13 RPM	477.68 RPM
bodymap2_thyroid	0.00 RPM	340.56 RPM
bodymap2_white_blood_cells	0.00 RPM	928.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_769 was not detected

EST

No EST(s) were mapped for retro_hsap_769 retrocopy.

TSS

No TSS is located nearby retro_hsap_769 retrocopy 5' end.

Lab

retro_hsap_769 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_769 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_538
Gorilla gorilla	retro_ggor_638

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 182 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Homo sapiens	ENSG00000109475	33 retrocopies	retro_hsap_1245, retro_hsap_126, retro_hsap_1265, retro_hsap_1417, retro_hsap_1636, retro_hsap_1735, retro_hsap_1756, retro_hsap_1921, retro_hsap_1987, retro_hsap_2041, retro_hsap_2145, retro_hsap_232, retro_hsap_2570, retro_hsap_258, retro_hsap_2624, retro_hsap_2695, retro_hsap_288, retro_hsap_2997, retro_hsap_3090, retro_hsap_3463, retro_hsap_3550, retro_hsap_3689, retro_hsap_4055, retro_hsap_4091, retro_hsap_4314, retro_hsap_520, retro_hsap_720, retro_hsap_769 , retro_hsap_830, retro_hsap_853, retro_hsap_927, retro_hsap_941, retro_hsap_977,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Myotis lucifugus	ENSMLUG00000000464	4 retrocopies	retro_mluc_125, retro_mluc_1372, retro_mluc_1427, retro_mluc_1847,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Rattus norvegicus	ENSRNOG00000016387	36 retrocopies	retro_rnor_1031, retro_rnor_1083, retro_rnor_1101, retro_rnor_1172, retro_rnor_1376, retro_rnor_1550, retro_rnor_1575, retro_rnor_1630, retro_rnor_1694, retro_rnor_1695, retro_rnor_1696, retro_rnor_1775, retro_rnor_1803, retro_rnor_1844, retro_rnor_1857, retro_rnor_2029, retro_rnor_2090, retro_rnor_2095, retro_rnor_2139, retro_rnor_2230, retro_rnor_2565, retro_rnor_2578, retro_rnor_2597, retro_rnor_2621, retro_rnor_2651, retro_rnor_2794, retro_rnor_282, retro_rnor_367, retro_rnor_500, retro_rnor_575, retro_rnor_605, retro_rnor_617, retro_rnor_672, retro_rnor_848, retro_rnor_866, retro_rnor_869,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Tarsius syrichta	ENSTSYG00000001781	34 retrocopies	retro_tsyr_1071, retro_tsyr_1087, retro_tsyr_1141, retro_tsyr_1249, retro_tsyr_1253, retro_tsyr_1292, retro_tsyr_1328, retro_tsyr_1375, retro_tsyr_140, retro_tsyr_1414, retro_tsyr_1425, retro_tsyr_1514, retro_tsyr_1573, retro_tsyr_164, retro_tsyr_1702, retro_tsyr_1849, retro_tsyr_2033, retro_tsyr_2035, retro_tsyr_2094, retro_tsyr_211, retro_tsyr_2172, retro_tsyr_220, retro_tsyr_221, retro_tsyr_254, retro_tsyr_300, retro_tsyr_375, retro_tsyr_49, retro_tsyr_59, retro_tsyr_597, retro_tsyr_678, retro_tsyr_812, retro_tsyr_853, retro_tsyr_872, retro_tsyr_897,
Tursiops truncatus	ENSTTRG00000003443	6 retrocopies	retro_ttru_1667, retro_ttru_1831, retro_ttru_355, retro_ttru_710, retro_ttru_717, retro_ttru_821,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.15 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.30 RPM
FIN_HG00277	0.26 RPM
FIN_HG00315	0.14 RPM
FIN_HG00321	0.39 RPM
FIN_HG00328	0.21 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.17 RPM
FIN_HG00375	0.17 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.29 RPM
GBR_HG00111	0.41 RPM
GBR_HG00114	0.29 RPM
GBR_HG00119	0.19 RPM
GBR_HG00131	0.23 RPM
GBR_HG00133	0.14 RPM
GBR_HG00134	0.26 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.50 RPM
GBR_HG00143	0.13 RPM
TSI_NA20512	0.28 RPM
TSI_NA20513	0.15 RPM
TSI_NA20518	0.17 RPM
TSI_NA20532	0.27 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.20 RPM
TSI_NA20765	0.25 RPM
TSI_NA20771	0.14 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.41 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.17 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.18 RPM

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Indel association:

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