RetrogeneDB ID: retro_hsap_153

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:52834347..52834914(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224680
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PLA2G12A
• Ensembl ID: ENSG00000123739
• Aliases: PLA2G12A, GXII, PLA2G12, ROSSY
• Description: phospholipase A2, group XIIA [Source:HGNC Symbol;Acc:18554]

Sequence

>retro_hsap_153
TTGGCCCTTCTCCCGCGCCCCGCGCTCACCCTCCTGCTCCTCCTCATGGCCGCTGTTATCAGGTGCCTGGAGCAGGCCTA
GACCACCGACTGGAGGGCCACCCTGAAGACCATCCGGAACGGCGTTCATAAGATAGACACGTACCTGAACGCCGCCTTGG
ACCTCCTGGGAGGCGAGGACGGTCTCTGCCAGTATAAATGCAGTGACGGATCTAAGCCTTTCCCACGTTATGGTTATAAA
CCCTCCCCACCGAATGGATGTGGCTCTCCACTGTTTGGCGTTCATCTTAACATTGGTATCCCTTCCCTGACAAAGTGTTG
CAACTAACACGACAGGTGCTATGAGAACTGTGGCAAAAGCAAGAATGACTGTGATGAGAAATTCCAGTATTGCCTCTCCA
AGATCTGCCGAGAAGTACAGAAAACACTAGGACTAACTTAGCATGTTCAGGCATGTGAAACAACAATGGAGCTCTTGTTT
GACAGTGTTATACATTTAGGTTGTAAACCATATCTGGACAGCCAACGAGCCACATGCAGGTGTCATTATGAAGAAAAAAC
CGATATT

Alignment

ORF - retro_hsap_153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALLSRPALTLLLLLMAAVVRCQEQAQTTDWRATLKTIRNGVHKIDTYLNAALDLLGGEDGLCQYKCSDG
          .ALL.RPALTLLLLLMAAV.RC.EQA.TTDWRATLKTIRNGVHKIDTYLNAALDLLGGEDGLCQYKCSDG
Retrocopy LALLPRPALTLLLLLMAAVIRCLEQA*TTDWRATLKTIRNGVHKIDTYLNAALDLLGGEDGLCQYKCSDG

Parental  SKPFPRYGYKPSPPNGCGSPLFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQYCLSKICRDVQ
          SKPFPRYGYKPSPPNGCGSPLFGVHLNIGIPSLTKCCN.HDRCYE.CGKSKNDCDE.FQYCLSKICR.VQ
Retrocopy SKPFPRYGYKPSPPNGCGSPLFGVHLNIGIPSLTKCCN*HDRCYENCGKSKNDCDEKFQYCLSKICREVQ

Parental  KTLGLTQHVQACETTVELLFDSVIHLGCKPYLDSQRAACRCHYEEKTDL
          KTLGLT.HVQACETT.ELLFDSVIHLGCKPYLDSQRA.CRCHYEEKTD.
Retrocopy KTLGLT*HVQACETTMELLFDSVIHLGCKPYLDSQRATCRCHYEEKTDI

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	30.55 RPM
bodymap2_adrenal	0.00 RPM	21.19 RPM
bodymap2_brain	0.16 RPM	54.36 RPM
bodymap2_breast	0.12 RPM	44.53 RPM
bodymap2_colon	0.10 RPM	35.15 RPM
bodymap2_heart	0.09 RPM	57.21 RPM
bodymap2_kidney	0.06 RPM	69.65 RPM
bodymap2_liver	0.02 RPM	48.67 RPM
bodymap2_lung	0.00 RPM	30.31 RPM
bodymap2_lymph_node	0.09 RPM	24.07 RPM
bodymap2_ovary	0.08 RPM	44.03 RPM
bodymap2_prostate	0.05 RPM	47.79 RPM
bodymap2_skeletal_muscle	0.05 RPM	22.10 RPM
bodymap2_testis	0.09 RPM	33.03 RPM
bodymap2_thyroid	0.23 RPM	46.02 RPM
bodymap2_white_blood_cells	0.16 RPM	22.21 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_153 in 7 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	1:52834025..52834455
ENCFF002CGN	POLR2A	1:52834189..52834316
ENCFF002CJE	POLR2A	1:52834189..52834423
ENCFF002CKX	POLR2A	1:52834163..52834308
ENCFF002CRK	POLR2A	1:52833977..52834501
ENCFF002CZC	POLR2A	1:52833996..52834536
ENCFF002CZD	POLR2A	1:52834021..52834531

EST

No EST(s) were mapped for retro_hsap_153 retrocopy.

TSS

No TSS is located nearby retro_hsap_153 retrocopy 5' end.

Lab

retro_hsap_153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_153 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_242

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172, retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153 ,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242, retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30, retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623, retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.17 RPM
CEU_NA11843	0.11 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.42 RPM
CEU_NA12400	0.21 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.14 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.17 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.28 RPM
FIN_HG00338	0.28 RPM
FIN_HG00349	0.20 RPM
FIN_HG00375	0.22 RPM
FIN_HG00377	0.23 RPM
FIN_HG00378	0.15 RPM
GBR_HG00099	0.23 RPM
GBR_HG00111	0.26 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.15 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.22 RPM
GBR_HG00143	0.35 RPM
TSI_NA20512	0.28 RPM
TSI_NA20513	0.24 RPM
TSI_NA20518	0.25 RPM
TSI_NA20532	0.37 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.15 RPM
TSI_NA20765	0.12 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.21 RPM
TSI_NA20798	0.28 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.18 RPM
YRI_NA19099	0.11 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.15 RPM
YRI_NA19213	0.10 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.24 RPM

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Indel association:

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