RetrogeneDB ID: retro_hsap_982

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:32050753..32051063(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000244436
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPLP2
• Ensembl ID: ENSG00000177600
• Aliases: None
• Description: ribosomal protein, large, P2 [Source:HGNC Symbol;Acc:10377]

Sequence

>retro_hsap_982
TCCTACCTACTGGCTGCCCTCGGGGGCAACCCCTTGCCCAGCACCAAGGACGTCAAGAAGATCCTGTACAATATAAGCAA
TAAGGCCAATGGCAACCAGTGCAGCAAGATCATCAGTGAGCTGAATGGAAAAAACATTAAAGGTGTCATTGCCCAGGGTA
TTGGCAAGTTGCCATTGTGCTCTCCCACAAGGCTGTGGCCGCCTCTGCTGCCCCGGCTCTGTAGCTCCTGCTGCTGGCCC
TGCCCCTACTACAAAGAAGAAGAAACATGAGAAGAAGGAGTCCCAAGAGTCACATGGTGACATATGATTT

Alignment

ORF - retro_hsap_982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.19 %
• Parental protein coverage: 92.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKL-ASVPAGGAVAVS
          SYLLAALGGN..PS.KD.KKIL......A......K.ISELNGKNI..VIAQGIGKL.A.V....AVA.S
Retrocopy SYLLAALGGNPLPSTKDVKKILYNISNKANGNQCSKIISELNGKNIKGVIAQGIGKL<AIVLSHKAVAAS

Parental  AA-PGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMGF
          AA.PGS.APAAG.AP.....KK...K.ES.ES..D..F
Retrocopy AA<PGSVAPAAGPAPTT--KKKKHEKKESQESHGDI*F

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	0.00 RPM	769.99 RPM
bodymap2_adrenal	0.00 RPM	769.69 RPM
bodymap2_brain	0.00 RPM	78.36 RPM
bodymap2_breast	0.00 RPM	533.43 RPM
bodymap2_colon	0.00 RPM	451.80 RPM
bodymap2_heart	0.00 RPM	108.53 RPM
bodymap2_kidney	0.00 RPM	199.53 RPM
bodymap2_liver	0.00 RPM	168.76 RPM
bodymap2_lung	0.00 RPM	559.32 RPM
bodymap2_lymph_node	0.00 RPM	783.63 RPM
bodymap2_ovary	0.00 RPM	579.04 RPM
bodymap2_prostate	0.00 RPM	606.29 RPM
bodymap2_skeletal_muscle	0.00 RPM	623.26 RPM
bodymap2_testis	0.00 RPM	296.18 RPM
bodymap2_thyroid	0.00 RPM	265.61 RPM
bodymap2_white_blood_cells	0.00 RPM	811.63 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_982 in 4 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CLM	POLR2A	12:32049417..32049957
ENCFF002CQA	POLR2A	12:32049221..32049791
ENCFF002CXQ	POLR2A	12:32050443..32051093
ENCFF002CZY	POLR2A	12:32049249..32049765
ENCFF002CZY	POLR2A	12:32050674..32051190

EST

No EST(s) were mapped for retro_hsap_982 retrocopy.

TSS

No TSS is located nearby retro_hsap_982 retrocopy 5' end.

Lab

retro_hsap_982 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_982 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_764

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001777	2 retrocopies	retro_btau_117, retro_btau_1399,
Canis familiaris	ENSCAFG00000009523	1 retrocopy	retro_cfam_18,
Ciona intestinalis	ENSCING00000000626	1 retrocopy	retro_cint_34,
Dipodomys ordii	ENSDORG00000016458	3 retrocopies	retro_dord_705, retro_dord_706, retro_dord_707,
Felis catus	ENSFCAG00000008417	1 retrocopy	retro_fcat_860,
Homo sapiens	ENSG00000177600	5 retrocopies	retro_hsap_1777, retro_hsap_3395, retro_hsap_3440, retro_hsap_821, retro_hsap_982 ,
Gorilla gorilla	ENSGGOG00000010789	5 retrocopies	retro_ggor_2238, retro_ggor_2298, retro_ggor_2323, retro_ggor_672, retro_ggor_784,
Mus musculus	ENSMUSG00000025508	4 retrocopies	retro_mmus_1364, retro_mmus_2111, retro_mmus_2282, retro_mmus_330,
Nomascus leucogenys	ENSNLEG00000026860	5 retrocopies	retro_nleu_1948, retro_nleu_2144, retro_nleu_2296, retro_nleu_2762, retro_nleu_85,
Otolemur garnettii	ENSOGAG00000016296	2 retrocopies	retro_ogar_156, retro_ogar_275,
Pongo abelii	ENSPPYG00000002885	6 retrocopies	retro_pabe_1537, retro_pabe_1543, retro_pabe_2789, retro_pabe_2844, retro_pabe_732, retro_pabe_830,
Pan troglodytes	ENSPTRG00000003137	5 retrocopies	retro_ptro_1189, retro_ptro_2307, retro_ptro_2332, retro_ptro_572, retro_ptro_764,
Rattus norvegicus	ENSRNOG00000002116	3 retrocopies	retro_rnor_257, retro_rnor_320, retro_rnor_388,
Sarcophilus harrisii	ENSSHAG00000001056	1 retrocopy	retro_shar_321,
Sus scrofa	ENSSSCG00000012842	1 retrocopy	retro_sscr_54,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 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	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.04 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	0.08 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.03 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	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 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).