RetrogeneDB ID: retro_hsap_117

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:16119298..16119781(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224321
• 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_117
AAGTTTGACCCCAGAGAGATCAAAGTTGTATACCTGAGGTGCACTGGAGGTGAAGTCGCTGCTTCTGCGCTGGCCCCCAA
GATCGGCCCCCTGGGTCTGTCTCCAAAAAAGGTTGGTGATAACATTGCCAAGGCAACGGGTTACCGGAAGGGCCTGAGGA
TTACAGTGAAACTGACCATTCAGAACAGACAGGCCCAGATTGAGGTGGTGCCTTCTGCCTCTGCCCTGATCATCAAAGCC
CTCAGGGAACCACTAAGAGACAGAAAGAAACAGAAAAACATTAAACACAGTGGGAATATCACTTTTGATGAGATCGTCAA
CATTGCTTGACACACGTGGCACCGATCTTTAGCCAGGGAACTCTCTGGAACCATTAAAGAGATCCTGGGGACTGCCCAGT
CTGTGGGCTGTAATGTTGATGGCCGCTACCCTCATGACATCATAGATGACATCAACAGTGGTGCTGTGGAATGCCCAGCC
AGT

Alignment

ORF - retro_hsap_117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.98 %
• Parental protein coverage: 98.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQIEV
          KFDP.EIKVVYLRCTGGEV.A.SALAPKIGPLGLSPKKVGD.IAKATG..KGLRITVKLTIQNRQAQIEV
Retrocopy KFDPREIKVVYLRCTGGEVAA-SALAPKIGPLGLSPKKVGDNIAKATGYRKGLRITVKLTIQNRQAQIEV

Parental  VPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNV
          VPSASALIIKAL.EP.RDRKKQKNIKHSGNITFDEIVNIA....HRSLARELSGTIKEILGTAQSVGCNV
Retrocopy VPSASALIIKALREPLRDRKKQKNIKHSGNITFDEIVNIA*HTWHRSLARELSGTIKEILGTAQSVGCNV

Parental  DGRHPHDIIDDINSGAVECPAS
          DGR.PHDIIDDINSGAVECPAS
Retrocopy DGRYPHDIIDDINSGAVECPAS

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	0.12 RPM	334.37 RPM
bodymap2_adrenal	0.06 RPM	375.59 RPM
bodymap2_brain	0.05 RPM	87.48 RPM
bodymap2_breast	0.62 RPM	274.19 RPM
bodymap2_colon	0.12 RPM	494.79 RPM
bodymap2_heart	0.00 RPM	91.33 RPM
bodymap2_kidney	0.04 RPM	286.03 RPM
bodymap2_liver	0.51 RPM	146.20 RPM
bodymap2_lung	0.00 RPM	420.61 RPM
bodymap2_lymph_node	0.00 RPM	493.85 RPM
bodymap2_ovary	0.10 RPM	470.84 RPM
bodymap2_prostate	0.00 RPM	765.31 RPM
bodymap2_skeletal_muscle	0.00 RPM	532.70 RPM
bodymap2_testis	0.04 RPM	314.22 RPM
bodymap2_thyroid	0.02 RPM	203.98 RPM
bodymap2_white_blood_cells	0.02 RPM	691.71 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_117 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CXQ	POLR2A	1:16118497..16119147

EST

No EST(s) were mapped for retro_hsap_117 retrocopy.

TSS

No TSS is located nearby retro_hsap_117 retrocopy 5' end.

Lab

retro_hsap_117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_117 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_221

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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	0.02 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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