RetrogeneDB ID: retro_hsap_1801

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:8102440..8102755(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000271002
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSG00000142676
• Aliases: RPL11, DBA7, GIG34, L11
• Description: ribosomal protein L11 [Source:HGNC Symbol;Acc:10301]

Sequence

>retro_hsap_1801
CAACTTTATATCTGTAAGCTCTGCCTCAATATCTGTGTGGAGAAGAGTGACGACAGACTGACACAGGCAGCCAAGGTGTT
GGAGCAACTCACAGGCCAGACCCCTGTGTTTTCCAAAACTAGATGCACTGTCAGATCTTTTGTTTTCAGGAGAAATGAAA
AGATTACTGTTGACTGCACAGTTCCAGGGGCCAAGGCAGAAGAAATCCTGGAGAAAGGTCCAAAGGTATGGGAGTATGAA
TTATTTTTTCTTAACTTCTCAGATACTGGAAACTTTGGTTTCCAGGAACACAAGAATCTGGGTATCAAATATGAA

Alignment

ORF - retro_hsap_1801 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.57 %
• Parental protein coverage: 61.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKIAVHCTVRGAKAEEIL
          .L.I.KLCLNICV..S.DRLT.AAKVLEQLTGQTPVFSK.R.TVRSF..RRNEKI.V.CTV.GAKAEEIL
Retrocopy QLYICKLCLNICVEKSDDRLTQAAKVLEQLTGQTPVFSKTRCTVRSFVFRRNEKITVDCTVPGAKAEEIL

Parental  EKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
          EKG.KV.EYEL...NFSDTGNFGF..QEH..LGIKY.
Retrocopy EKGPKVWEYELFFLNFSDTGNFGF--QEHKNLGIKYE

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	0.04 RPM	970.38 RPM
bodymap2_adrenal	0.10 RPM	1130.92 RPM
bodymap2_brain	0.00 RPM	214.62 RPM
bodymap2_breast	0.08 RPM	661.00 RPM
bodymap2_colon	0.10 RPM	947.57 RPM
bodymap2_heart	0.00 RPM	210.62 RPM
bodymap2_kidney	0.00 RPM	373.41 RPM
bodymap2_liver	0.00 RPM	317.51 RPM
bodymap2_lung	0.07 RPM	912.03 RPM
bodymap2_lymph_node	0.00 RPM	994.96 RPM
bodymap2_ovary	0.00 RPM	1227.26 RPM
bodymap2_prostate	0.03 RPM	1177.85 RPM
bodymap2_skeletal_muscle	0.00 RPM	396.86 RPM
bodymap2_testis	0.00 RPM	630.41 RPM
bodymap2_thyroid	0.28 RPM	607.33 RPM
bodymap2_white_blood_cells	0.00 RPM	1137.36 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_1801 in 38 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	17:8103435..8103801
ENCFF002CFX	POLR2A	17:8103430..8103836
ENCFF002CGN	POLR2A	17:8103606..8103759
ENCFF002CHO	POLR2A	17:8103386..8103842
ENCFF002CIO	POLR2A	17:8103533..8103751
ENCFF002CJE	POLR2A	17:8103311..8103947
ENCFF002CJZ	POLR2A	17:8103336..8103819
ENCFF002CKX	POLR2A	17:8103468..8103726
ENCFF002CLM	POLR2A	17:8103234..8103774
ENCFF002COJ	POLR2A	17:8103438..8103874
ENCFF002CPG	POLR2A	17:8103626..8103789
ENCFF002CPH	POLR2A	17:8103494..8103884
ENCFF002CQA	POLR2A	17:8103330..8103801
ENCFF002CQC	POLR2A	17:8103663..8103794
ENCFF002CQE	POLR2A	17:8103451..8103801
ENCFF002CQG	POLR2A	17:8103625..8103777
ENCFF002CQI	POLR2A	17:8103478..8103691
ENCFF002CQK	POLR2A	17:8103445..8103814
ENCFF002CQM	POLR2A	17:8103492..8103803
ENCFF002CQO	POLR2A	17:8103498..8103774
ENCFF002CRK	POLR2A	17:8103253..8103777
ENCFF002CSY	POLR2A	17:8103236..8103926
ENCFF002CXM	POLR2A	17:8103440..8103930
ENCFF002CXO	POLR2A	17:8103467..8103891
ENCFF002CXP	POLR2A	17:8103427..8103907
ENCFF002CZC	POLR2A	17:8103431..8103804
ENCFF002CZD	POLR2A	17:8103485..8103780
ENCFF002CZW	POLR2A	17:8103122..8103872
ENCFF002CZY	POLR2A	17:8103375..8103791
ENCFF002DAE	POLR2A	17:8103524..8103834
ENCFF002DAH	POLR2A	17:8103476..8103760
ENCFF002DAK	POLR2A	17:8103367..8103867
ENCFF002DAV	POLR2A	17:8103398..8103942
ENCFF002DBB	POLR2A	17:8103584..8103784
ENCFF002DBE	POLR2A	17:8103421..8103917
ENCFF002DBO	POLR2A	17:8103632..8103742
ENCFF002DBP	POLR2A	17:8103519..8103746
ENCFF002DBQ	POLR2A	17:8103497..8103867

EST

No EST(s) were mapped for retro_hsap_1801 retrocopy.

TSS

No TSS is located nearby retro_hsap_1801 retrocopy 5' end.

Lab

retro_hsap_1801 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1801 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1325
Pongo abelii	retro_pabe_1478

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020905	1 retrocopy	retro_btau_267,
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Callithrix jacchus	ENSCJAG00000020953	1 retrocopy	retro_cjac_790,
Dasypus novemcinctus	ENSDNOG00000011230	2 retrocopies	retro_dnov_1453, retro_dnov_605,
Homo sapiens	ENSG00000142676	6 retrocopies	retro_hsap_1159, retro_hsap_1801 , retro_hsap_2272, retro_hsap_3238, retro_hsap_606, retro_hsap_712,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Loxodonta africana	ENSLAFG00000030853	2 retrocopies	retro_lafr_371, retro_lafr_434,
Macropus eugenii	ENSMEUG00000013738	3 retrocopies	retro_meug_488, retro_meug_517, retro_meug_633,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica	ENSMODG00000012828	1 retrocopy	retro_mdom_641,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus	ENSOANG00000000321	1 retrocopy	retro_oana_49,
Oryctolagus cuniculus	ENSOCUG00000022928	1 retrocopy	retro_ocun_1387,
Pongo abelii	ENSPPYG00000001736	6 retrocopies	retro_pabe_1478, retro_pabe_1946, retro_pabe_2686, retro_pabe_612, retro_pabe_615, retro_pabe_964,
Pteropus vampyrus	ENSPVAG00000004282	1 retrocopy	retro_pvam_1068,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Sus scrofa	ENSSSCG00000024260	4 retrocopies	retro_sscr_1048, retro_sscr_1049, retro_sscr_1074, retro_sscr_819,
Tarsius syrichta	ENSTSYG00000001349	6 retrocopies	retro_tsyr_1138, retro_tsyr_127, retro_tsyr_1583, retro_tsyr_1605, retro_tsyr_516, retro_tsyr_520,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.15 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.13 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.10 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.06 RPM

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Indel association:

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