RetrogeneDB ID: retro_hsap_3545

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:171054608..171055065(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000219814
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL23A
• Ensembl ID: ENSG00000198242
• Aliases: None
• Description: ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]

Sequence

>retro_hsap_3545
GCACCGAAAGCGAAGGAAGCTCCTGCTCCTCCTAAAGCCGAAGCCAAAGTGAAGGTTTTAAAGGCCAAGAAGGCAGTGTT
GAAAGGTGTCCGCAGCCACACGCAAAAAAGAAGATCCGCATGTCACCCACCTTCAGGCGGCCCAAGACACTGCGACTCCG
GAGGCAGCCCAGATATCCTCGGAAGAGCACCCCCAGGAGAAACAAGCTTGGCCACTATGCTATCATCAAGTTTCCGCTGA
CCACTGAGTCGGCCGGAAGAAGATAGAAGAAAACAACACGCTTGTGTTCACTGTGGATGTTAAAGCCAACAAGCACCAGA
TCAGACAGGCTGTGAAGAAGCTCTATGACAGTGATGTGGCCAAGGTCACCACCCTGATTTGTCCTGATAAAGAGAACAAG
GCATATGTTCGACTTGCTCCTGATTATGATGCTTTCGATGTTGTAACAAAATTGGGA

Alignment

ORF - retro_hsap_3545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.28 %
• Parental protein coverage: 98.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  APKAKKEAPAPPKAEA-KAKALKAKK-AVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRN
          APKAK.EAPAPPKAEA......K.....V......H.KKKIR.SPTFRRPKTLRLRRQP.YPRKS.PRRN
Retrocopy APKAK-EAPAPPKAEA<QSEGFKGQEGSVERCPQPHAKKKIRMSPTFRRPKTLRLRRQPRYPRKSTPRRN

Parental  KLDHYAIIKFPLTTESA-MKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYV
          KL.HYAIIKFPLTTESA..KKIE.NNTLVF.VDVKANKHQI.QAVKKLYD.DVAKV.TLI.PD.E.KAYV
Retrocopy KLGHYAIIKFPLTTESA<RKKIEENNTLVFTVDVKANKHQIRQAVKKLYDSDVAKVTTLICPDKENKAYV

Parental  RLAPDYDALDVANKIG
          RLAPDYDA.DV..K.G
Retrocopy RLAPDYDAFDVVTKLG

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	0.08 RPM	192.56 RPM
bodymap2_adrenal	0.02 RPM	242.36 RPM
bodymap2_brain	0.00 RPM	43.88 RPM
bodymap2_breast	0.00 RPM	119.40 RPM
bodymap2_colon	0.15 RPM	221.12 RPM
bodymap2_heart	0.00 RPM	56.34 RPM
bodymap2_kidney	0.00 RPM	85.35 RPM
bodymap2_liver	0.00 RPM	67.28 RPM
bodymap2_lung	0.00 RPM	194.32 RPM
bodymap2_lymph_node	0.00 RPM	239.11 RPM
bodymap2_ovary	0.04 RPM	286.76 RPM
bodymap2_prostate	0.00 RPM	296.99 RPM
bodymap2_skeletal_muscle	0.00 RPM	185.41 RPM
bodymap2_testis	0.02 RPM	126.20 RPM
bodymap2_thyroid	0.00 RPM	127.58 RPM
bodymap2_white_blood_cells	0.00 RPM	333.55 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3545 was not detected

EST

No EST(s) were mapped for retro_hsap_3545 retrocopy.

TSS

No TSS is located nearby retro_hsap_3545 retrocopy 5' end.

Lab

retro_hsap_3545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3545 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 274 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046394	6 retrocopies	retro_btau_132, retro_btau_159, retro_btau_169, retro_btau_178, retro_btau_237, retro_btau_8,
Callithrix jacchus	ENSCJAG00000013126	7 retrocopies	retro_cjac_118, retro_cjac_154, retro_cjac_20, retro_cjac_258, retro_cjac_30, retro_cjac_315, retro_cjac_46,
Felis catus	ENSFCAG00000004021	35 retrocopies	retro_fcat_1003, retro_fcat_1011, retro_fcat_1030, retro_fcat_1039, retro_fcat_1054, retro_fcat_1071, retro_fcat_1073, retro_fcat_11, retro_fcat_1124, retro_fcat_1161, retro_fcat_1202, retro_fcat_1205, retro_fcat_1275, retro_fcat_1389, retro_fcat_1659, retro_fcat_1670, retro_fcat_1748, retro_fcat_1787, retro_fcat_1796, retro_fcat_1810, retro_fcat_182, retro_fcat_185, retro_fcat_1856, retro_fcat_1905, retro_fcat_1909, retro_fcat_1944, retro_fcat_2022, retro_fcat_289, retro_fcat_364, retro_fcat_476, retro_fcat_603, retro_fcat_657, retro_fcat_765, retro_fcat_898, retro_fcat_950,
Homo sapiens	ENSG00000198242	57 retrocopies	retro_hsap_110, retro_hsap_1139, retro_hsap_1177, retro_hsap_1315, retro_hsap_1316, retro_hsap_1460, retro_hsap_1616, retro_hsap_1660, retro_hsap_1714, retro_hsap_1775, retro_hsap_1791, retro_hsap_1807, retro_hsap_1833, retro_hsap_1924, retro_hsap_1970, retro_hsap_2021, retro_hsap_2024, retro_hsap_2134, retro_hsap_2169, retro_hsap_2210, retro_hsap_2222, retro_hsap_2271, retro_hsap_2310, retro_hsap_2356, retro_hsap_2359, retro_hsap_2390, retro_hsap_2404, retro_hsap_2446, retro_hsap_2509, retro_hsap_2511, retro_hsap_2528, retro_hsap_2567, retro_hsap_2602, retro_hsap_2629, retro_hsap_2748, retro_hsap_2804, retro_hsap_2874, retro_hsap_3282, retro_hsap_334, retro_hsap_3377, retro_hsap_341, retro_hsap_342, retro_hsap_345, retro_hsap_3545 , retro_hsap_3571, retro_hsap_3815, retro_hsap_4118, retro_hsap_4127, retro_hsap_4329, retro_hsap_490, retro_hsap_504, retro_hsap_641, retro_hsap_672, retro_hsap_725, retro_hsap_751, retro_hsap_775, retro_hsap_945,
Gorilla gorilla	ENSGGOG00000016736	26 retrocopies	retro_ggor_1027, retro_ggor_1028, retro_ggor_1123, retro_ggor_120, retro_ggor_123, retro_ggor_1284, retro_ggor_140, retro_ggor_1431, retro_ggor_158, retro_ggor_1650, retro_ggor_1743, retro_ggor_1789, retro_ggor_1911, retro_ggor_1948, retro_ggor_2164, retro_ggor_2239, retro_ggor_2285, retro_ggor_229, retro_ggor_2409, retro_ggor_2475, retro_ggor_2568, retro_ggor_2764, retro_ggor_2773, retro_ggor_580, retro_ggor_611, retro_ggor_642,
Loxodonta africana	ENSLAFG00000013387	16 retrocopies	retro_lafr_1176, retro_lafr_153, retro_lafr_237, retro_lafr_33, retro_lafr_335, retro_lafr_442, retro_lafr_510, retro_lafr_525, retro_lafr_551, retro_lafr_557, retro_lafr_643, retro_lafr_78, retro_lafr_891, retro_lafr_908, retro_lafr_957, retro_lafr_96,
Myotis lucifugus	ENSMLUG00000012448	4 retrocopies	retro_mluc_175, retro_mluc_2375, retro_mluc_353, retro_mluc_91,
Monodelphis domestica	ENSMODG00000019297	3 retrocopies	retro_mdom_120, retro_mdom_870, retro_mdom_912,
Mustela putorius furo	ENSMPUG00000014179	12 retrocopies	retro_mputfur_102, retro_mputfur_106, retro_mputfur_123, retro_mputfur_159, retro_mputfur_168, retro_mputfur_179, retro_mputfur_3, retro_mputfur_333, retro_mputfur_42, retro_mputfur_52, retro_mputfur_599, retro_mputfur_91,
Mus musculus	ENSMUSG00000058546	8 retrocopies	retro_mmus_1, retro_mmus_126, retro_mmus_130, retro_mmus_184, retro_mmus_224, retro_mmus_64, retro_mmus_84, retro_mmus_95,
Pongo abelii	ENSPPYG00000008108	49 retrocopies	retro_pabe_1030, retro_pabe_1203, retro_pabe_1206, retro_pabe_1335, retro_pabe_1430, retro_pabe_1459, retro_pabe_1590, retro_pabe_1721, retro_pabe_1747, retro_pabe_1752, retro_pabe_1766, retro_pabe_1797, retro_pabe_1846, retro_pabe_1848, retro_pabe_1867, retro_pabe_1926, retro_pabe_1947, retro_pabe_1995, retro_pabe_2018, retro_pabe_2057, retro_pabe_2075, retro_pabe_2082, retro_pabe_2091, retro_pabe_2132, retro_pabe_2156, retro_pabe_2221, retro_pabe_2334, retro_pabe_234, retro_pabe_243, retro_pabe_2612, retro_pabe_2738, retro_pabe_2773, retro_pabe_2820, retro_pabe_2944, retro_pabe_3006, retro_pabe_3036, retro_pabe_3200, retro_pabe_3371, retro_pabe_3477, retro_pabe_351, retro_pabe_3528, retro_pabe_354, retro_pabe_474, retro_pabe_627, retro_pabe_754, retro_pabe_765, retro_pabe_799, retro_pabe_946, retro_pabe_984,
Rattus norvegicus	ENSRNOG00000023344	6 retrocopies	retro_rnor_136, retro_rnor_145, retro_rnor_211, retro_rnor_40, retro_rnor_404, retro_rnor_62,
Sarcophilus harrisii	ENSSHAG00000014549	13 retrocopies	retro_shar_188, retro_shar_373, retro_shar_407, retro_shar_448, retro_shar_498, retro_shar_564, retro_shar_624, retro_shar_630, retro_shar_685, retro_shar_698, retro_shar_824, retro_shar_829, retro_shar_835,
Sus scrofa	ENSSSCG00000017768	9 retrocopies	retro_sscr_1025, retro_sscr_1047, retro_sscr_1133, retro_sscr_239, retro_sscr_356, retro_sscr_418, retro_sscr_598, retro_sscr_638, retro_sscr_952,
Ictidomys tridecemlineatus	ENSSTOG00000011328	23 retrocopies	retro_itri_1022, retro_itri_1035, retro_itri_1051, retro_itri_1059, retro_itri_1071, retro_itri_1150, retro_itri_1261, retro_itri_1327, retro_itri_1347, retro_itri_1460, retro_itri_1507, retro_itri_217, retro_itri_225, retro_itri_304, retro_itri_360, retro_itri_494, retro_itri_626, retro_itri_627, retro_itri_734, retro_itri_761, retro_itri_791, retro_itri_965, retro_itri_972,

Population studies

Expression level across human populations :

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	0.04 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	0.00 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

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Indel association:

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