RetrogeneDB ID: retro_hsap_3422

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:12514341..12514953(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000212802
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL15
• Ensembl ID: ENSG00000174748
• Aliases: RPL15, DBA12, EC45, L15, RPL10, RPLY10, RPYL10
• Description: ribosomal protein L15 [Source:HGNC Symbol;Acc:10306]

Sequence

>retro_hsap_3422
ATGGGTGCATACAAGTACATCCAGGAGCTATGGAGAAAGAAGCAGTCTGATGTCATGCGCTTTCTTCTGAGGGTCCGCTG
CTGGCAGTACCGCCAGCTCTCTGCTCTCCACAGGGCTCCCCGCCCCACCCGGCCTGATAAAGCGCGCCGACTGGGCTACA
AGGCCAAGCAAGGTTACGTTATATATAGGATTCGTGTTCGCCGTGGTGGCCGAAAACGCCCAGTTCCTAAGGGTGCAACT
TACGGCAAGCCTGTCCATCATGGTGTTAACCAGCTAAAGTTTGCTCGAAGCCTTCAGTCCGTTGCAGAGGAGCGAGTTGG
ACGCCACTGTGGGGCTCTGAGGGTCCTGAATTCTTACTGGGTTGGTGAAGATTCCACATACAAATTTTTTGAGGTTATCC
TCATTGATCCATTCCATAAAGCTATCAGAAGAAATCCTGACACCCAGTGGATCACCAAACCAGTCCACAAGCACAGGGAG
ATGCGTGGGCTGACATCTGCAGGCCGAAAGAGCCGTGGCCTTGGAAAGGGCCATAAGTTCCACCACACTATTGGTGGCTC
TCGCCGGGCAGCTTGGAGAAGGCGCAATACTCTCCAGCTCCACCGTTACCGC

Alignment

ORF - retro_hsap_3422 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGG
          MGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGG
Retrocopy MGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGG

Parental  RKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHK
          RKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEER.GRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHK
Retrocopy RKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERVGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHK

Parental  AIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLHRYR
          AIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLHRYR
Retrocopy AIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLHRYR

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	0.38 RPM	613.95 RPM
bodymap2_adrenal	1.27 RPM	761.12 RPM
bodymap2_brain	0.33 RPM	581.06 RPM
bodymap2_breast	0.82 RPM	564.73 RPM
bodymap2_colon	1.72 RPM	864.33 RPM
bodymap2_heart	0.24 RPM	276.38 RPM
bodymap2_kidney	0.33 RPM	437.95 RPM
bodymap2_liver	0.36 RPM	306.40 RPM
bodymap2_lung	0.76 RPM	996.54 RPM
bodymap2_lymph_node	0.80 RPM	926.31 RPM
bodymap2_ovary	1.14 RPM	1298.03 RPM
bodymap2_prostate	1.78 RPM	1288.84 RPM
bodymap2_skeletal_muscle	1.91 RPM	589.94 RPM
bodymap2_testis	0.53 RPM	602.34 RPM
bodymap2_thyroid	0.92 RPM	616.52 RPM
bodymap2_white_blood_cells	1.36 RPM	1141.99 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3422 was not detected

EST

No EST(s) were mapped for retro_hsap_3422 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_158636	501 libraries	654 libraries	553 libraries	75 libraries	46 libraries

The graphical summary, for retro_hsap_3422 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_3422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3422 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 116 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033080	2 retrocopies	retro_btau_152, retro_btau_201,
Canis familiaris	ENSCAFG00000005764	5 retrocopies	retro_cfam_1003, retro_cfam_1159, retro_cfam_1630, retro_cfam_572, retro_cfam_656,
Cavia porcellus	ENSCPOG00000002253	4 retrocopies	retro_cpor_620, retro_cpor_807, retro_cpor_900, retro_cpor_978,
Felis catus	ENSFCAG00000026237	6 retrocopies	retro_fcat_1820, retro_fcat_285, retro_fcat_306, retro_fcat_610, retro_fcat_930, retro_fcat_985,
Homo sapiens	ENSG00000174748	14 retrocopies	retro_hsap_1294, retro_hsap_1804, retro_hsap_2160, retro_hsap_2870, retro_hsap_2927, retro_hsap_3095, retro_hsap_3422 , retro_hsap_3661, retro_hsap_3792, retro_hsap_592, retro_hsap_631, retro_hsap_791, retro_hsap_930, retro_hsap_957,
Gorilla gorilla	ENSGGOG00000024274	13 retrocopies	retro_ggor_1327, retro_ggor_1611, retro_ggor_1716, retro_ggor_1989, retro_ggor_2029, retro_ggor_2125, retro_ggor_2314, retro_ggor_2473, retro_ggor_39, retro_ggor_524, retro_ggor_552, retro_ggor_654, retro_ggor_771,
Myotis lucifugus	ENSMLUG00000013809	15 retrocopies	retro_mluc_1357, retro_mluc_1709, retro_mluc_1720, retro_mluc_2052, retro_mluc_2142, retro_mluc_2454, retro_mluc_425, retro_mluc_623, retro_mluc_701, retro_mluc_714, retro_mluc_748, retro_mluc_749, retro_mluc_907, retro_mluc_943, retro_mluc_99,
Macaca mulatta	ENSMMUG00000006353	1 retrocopy	retro_mmul_209,
Monodelphis domestica	ENSMODG00000014880	3 retrocopies	retro_mdom_1315, retro_mdom_1803, retro_mdom_918,
Mustela putorius furo	ENSMPUG00000012148	7 retrocopies	retro_mputfur_1011, retro_mputfur_1252, retro_mputfur_1291, retro_mputfur_314, retro_mputfur_346, retro_mputfur_658, retro_mputfur_669,
Mus musculus	ENSMUSG00000012405	2 retrocopies	retro_mmus_118, retro_mmus_8,
Nomascus leucogenys	ENSNLEG00000003580	1 retrocopy	retro_nleu_80,
Oryctolagus cuniculus	ENSOCUG00000010961	2 retrocopies	retro_ocun_215, retro_ocun_228,
Otolemur garnettii	ENSOGAG00000013056	13 retrocopies	retro_ogar_1066, retro_ogar_1129, retro_ogar_1182, retro_ogar_1453, retro_ogar_1483, retro_ogar_1629, retro_ogar_1809, retro_ogar_2378, retro_ogar_270, retro_ogar_3058, retro_ogar_3096, retro_ogar_3349, retro_ogar_903,
Procavia capensis	ENSPCAG00000011995	1 retrocopy	retro_pcap_265,
Rattus norvegicus	ENSRNOG00000008140	17 retrocopies	retro_rnor_1046, retro_rnor_1409, retro_rnor_1497, retro_rnor_1685, retro_rnor_1690, retro_rnor_1785, retro_rnor_2042, retro_rnor_2249, retro_rnor_2313, retro_rnor_2451, retro_rnor_2473, retro_rnor_2786, retro_rnor_2997, retro_rnor_428, retro_rnor_66, retro_rnor_710, retro_rnor_844,
Sus scrofa	ENSSSCG00000028079	5 retrocopies	retro_sscr_1219, retro_sscr_1225, retro_sscr_448, retro_sscr_968, retro_sscr_997,
Tursiops truncatus	ENSTTRG00000007244	5 retrocopies	retro_ttru_1305, retro_ttru_1358, retro_ttru_280, retro_ttru_920, retro_ttru_987,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	7.90 RPM
CEU_NA11843	5.94 RPM
CEU_NA11930	8.87 RPM
CEU_NA12004	3.61 RPM
CEU_NA12400	5.79 RPM
CEU_NA12751	4.23 RPM
CEU_NA12760	9.39 RPM
CEU_NA12827	6.70 RPM
CEU_NA12872	4.79 RPM
CEU_NA12873	7.69 RPM
FIN_HG00183	7.96 RPM
FIN_HG00277	6.03 RPM
FIN_HG00315	4.42 RPM
FIN_HG00321	3.63 RPM
FIN_HG00328	3.69 RPM
FIN_HG00338	4.43 RPM
FIN_HG00349	7.71 RPM
FIN_HG00375	5.55 RPM
FIN_HG00377	4.79 RPM
FIN_HG00378	4.59 RPM
GBR_HG00099	6.07 RPM
GBR_HG00111	5.37 RPM
GBR_HG00114	4.34 RPM
GBR_HG00119	3.88 RPM
GBR_HG00131	3.97 RPM
GBR_HG00133	4.12 RPM
GBR_HG00134	3.39 RPM
GBR_HG00137	6.60 RPM
GBR_HG00142	4.67 RPM
GBR_HG00143	5.49 RPM
TSI_NA20512	5.60 RPM
TSI_NA20513	4.28 RPM
TSI_NA20518	6.44 RPM
TSI_NA20532	4.93 RPM
TSI_NA20538	4.42 RPM
TSI_NA20756	7.22 RPM
TSI_NA20765	2.59 RPM
TSI_NA20771	6.55 RPM
TSI_NA20786	3.82 RPM
TSI_NA20798	4.37 RPM
YRI_NA18870	7.21 RPM
YRI_NA18907	4.12 RPM
YRI_NA18916	3.60 RPM
YRI_NA19093	5.13 RPM
YRI_NA19099	4.85 RPM
YRI_NA19114	4.14 RPM
YRI_NA19118	6.86 RPM
YRI_NA19213	2.89 RPM
YRI_NA19214	2.93 RPM
YRI_NA19223	4.70 RPM

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Indel association:

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