RetrogeneDB ID: retro_hsap_2436

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:53691182..53691676(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000185834
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL12
• Ensembl ID: ENSG00000197958
• Aliases: RPL12, L12
• Description: ribosomal protein L12 [Source:HGNC Symbol;Acc:10302]

Sequence

>retro_hsap_2436
ATGCCGCCGAAGTTCGACCCCAACGAGATCAAAGTCGTATACCTGAGGTGCACCGGAGGTGAAGTCGGTGCCACTTCTGC
CCTGGCCCCCAAGATCGGCCCCCTGTGTCTGTCTCCAAAAAAGGTTGGTGATGACATTGCCAAGGCAACGGTGACTGGAA
GGGCCTGAGGATTACAGTGAAACTGACCATTCAGAACAGACAGGCCCAGATTGAGGTGGTGCCTTCTGCCTCTGCCCTGA
TCATCAAAGCCCTCAAGGAACCACCAAGAGACAGAAAGAAACAGAAAAACATTAAACACAGTGGGAATATCACTTTTGAT
GAGATCGTCAACATTGCTCGACAGATGCGGCACCGATCCTTAGCCAGAGAACTCTCTGGAACCATTAAAGAGATCCTGGG
GACTGCCCAGTCTGTGGGCTGTAATGTTGATGGCCGCCACCCTCATGACATCATAGATGACATCAACAGTGGTGCTGTGG
AATGCCCAGCCAGT

Alignment

ORF - retro_hsap_2436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKAT-GDWKGLRITVKLTIQNRQA
          MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPL.LSPKKVGDDIAKAT.GDWKGLRITVKLTIQNRQA
Retrocopy MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLCLSPKKVGDDIAKAT<GDWKGLRITVKLTIQNRQA

Parental  QIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSV
          QIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSV
Retrocopy QIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSV

Parental  GCNVDGRHPHDIIDDINSGAVECPAS
          GCNVDGRHPHDIIDDINSGAVECPAS
Retrocopy GCNVDGRHPHDIIDDINSGAVECPAS

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	0.22 RPM	334.37 RPM
bodymap2_adrenal	0.10 RPM	375.59 RPM
bodymap2_brain	0.02 RPM	87.48 RPM
bodymap2_breast	0.06 RPM	274.19 RPM
bodymap2_colon	0.06 RPM	494.79 RPM
bodymap2_heart	0.02 RPM	91.33 RPM
bodymap2_kidney	0.10 RPM	286.03 RPM
bodymap2_liver	0.02 RPM	146.20 RPM
bodymap2_lung	0.21 RPM	420.61 RPM
bodymap2_lymph_node	0.07 RPM	493.85 RPM
bodymap2_ovary	0.12 RPM	470.84 RPM
bodymap2_prostate	0.59 RPM	765.31 RPM
bodymap2_skeletal_muscle	0.42 RPM	532.70 RPM
bodymap2_testis	0.08 RPM	314.22 RPM
bodymap2_thyroid	0.11 RPM	203.98 RPM
bodymap2_white_blood_cells	0.18 RPM	691.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2436 was not detected

EST

No EST(s) were mapped for retro_hsap_2436 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_102559	1119 libraries	644 libraries	64 libraries	1 library	1 library

The graphical summary, for retro_hsap_2436 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_2436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2436 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 151 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006963	3 retrocopies	retro_btau_102, retro_btau_2, retro_btau_5,
Callithrix jacchus	ENSCJAG00000018082	1 retrocopy	retro_cjac_221,
Homo sapiens	ENSG00000197958	41 retrocopies	retro_hsap_1064, retro_hsap_117, retro_hsap_1210, retro_hsap_127, retro_hsap_1311, retro_hsap_1359, retro_hsap_137, retro_hsap_1401, retro_hsap_1592, retro_hsap_1644, retro_hsap_1790, retro_hsap_1850, retro_hsap_1880, retro_hsap_1895, retro_hsap_2005, retro_hsap_2031, retro_hsap_2099, retro_hsap_2123, retro_hsap_2202, retro_hsap_2311, retro_hsap_2381, retro_hsap_2428, retro_hsap_2436 , retro_hsap_2456, retro_hsap_2642, retro_hsap_3388, retro_hsap_3405, retro_hsap_3458, retro_hsap_3544, retro_hsap_3578, retro_hsap_3709, retro_hsap_4107, retro_hsap_4121, retro_hsap_4746, retro_hsap_584, retro_hsap_643, retro_hsap_705, retro_hsap_719, retro_hsap_768, retro_hsap_868, retro_hsap_983,
Latimeria chalumnae	ENSLACG00000015373	3 retrocopies	retro_lcha_31, retro_lcha_87, retro_lcha_92,
Macropus eugenii	ENSMEUG00000007380	12 retrocopies	retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Macaca mulatta	ENSMMUG00000000422	2 retrocopies	retro_mmul_1823, retro_mmul_53,
Monodelphis domestica	ENSMODG00000004571	9 retrocopies	retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Mus musculus	ENSMUSG00000038900	1 retrocopy	retro_mmus_28,
Oryctolagus cuniculus	ENSOCUG00000004902	9 retrocopies	retro_ocun_1246, retro_ocun_1632, retro_ocun_1895, retro_ocun_318, retro_ocun_329, retro_ocun_520, retro_ocun_556, retro_ocun_677, retro_ocun_880,
Ochotona princeps	ENSOPRG00000011078	21 retrocopies	retro_opri_100, retro_opri_1018, retro_opri_1066, retro_opri_1110, retro_opri_1210, retro_opri_1217, retro_opri_221, retro_opri_265, retro_opri_336, retro_opri_353, retro_opri_418, retro_opri_461, retro_opri_479, retro_opri_576, retro_opri_638, retro_opri_648, retro_opri_658, retro_opri_672, retro_opri_835, retro_opri_905, retro_opri_986,
Pongo abelii	ENSPPYG00000019622	44 retrocopies	retro_pabe_1009, retro_pabe_1084, retro_pabe_1095, retro_pabe_1127, retro_pabe_1159, retro_pabe_1223, retro_pabe_1246, retro_pabe_1309, retro_pabe_1361, retro_pabe_1471, retro_pabe_1509, retro_pabe_1577, retro_pabe_1659, retro_pabe_1660, retro_pabe_1736, retro_pabe_1794, retro_pabe_1806, retro_pabe_1820, retro_pabe_1969, retro_pabe_1982, retro_pabe_2000, retro_pabe_2149, retro_pabe_2328, retro_pabe_2531, retro_pabe_2802, retro_pabe_2859, retro_pabe_2928, retro_pabe_2947, retro_pabe_3002, retro_pabe_3146, retro_pabe_3185, retro_pabe_3276, retro_pabe_3363, retro_pabe_3405, retro_pabe_3482, retro_pabe_3693, retro_pabe_488, retro_pabe_521, retro_pabe_604, retro_pabe_620, retro_pabe_757, retro_pabe_815, retro_pabe_831, retro_pabe_904,
Pan troglodytes	ENSPTRG00000022808	1 retrocopy	retro_ptro_21,
Rattus norvegicus	ENSRNOG00000016220	4 retrocopies	retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.43 RPM
CEU_NA11843	3.38 RPM
CEU_NA11930	4.14 RPM
CEU_NA12004	1.56 RPM
CEU_NA12400	2.49 RPM
CEU_NA12751	1.55 RPM
CEU_NA12760	3.86 RPM
CEU_NA12827	2.83 RPM
CEU_NA12872	1.44 RPM
CEU_NA12873	1.40 RPM
FIN_HG00183	2.55 RPM
FIN_HG00277	2.66 RPM
FIN_HG00315	1.96 RPM
FIN_HG00321	1.84 RPM
FIN_HG00328	0.90 RPM
FIN_HG00338	1.87 RPM
FIN_HG00349	3.22 RPM
FIN_HG00375	2.74 RPM
FIN_HG00377	1.61 RPM
FIN_HG00378	1.74 RPM
GBR_HG00099	1.48 RPM
GBR_HG00111	1.10 RPM
GBR_HG00114	1.29 RPM
GBR_HG00119	1.96 RPM
GBR_HG00131	1.32 RPM
GBR_HG00133	1.69 RPM
GBR_HG00134	1.24 RPM
GBR_HG00137	1.62 RPM
GBR_HG00142	1.81 RPM
GBR_HG00143	1.28 RPM
TSI_NA20512	1.36 RPM
TSI_NA20513	1.16 RPM
TSI_NA20518	5.13 RPM
TSI_NA20532	1.50 RPM
TSI_NA20538	2.12 RPM
TSI_NA20756	2.30 RPM
TSI_NA20765	0.73 RPM
TSI_NA20771	1.67 RPM
TSI_NA20786	1.57 RPM
TSI_NA20798	0.94 RPM
YRI_NA18870	2.37 RPM
YRI_NA18907	1.21 RPM
YRI_NA18916	1.35 RPM
YRI_NA19093	0.73 RPM
YRI_NA19099	1.68 RPM
YRI_NA19114	1.42 RPM
YRI_NA19118	1.20 RPM
YRI_NA19213	1.20 RPM
YRI_NA19214	0.81 RPM
YRI_NA19223	0.76 RPM

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Indel association:

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