RetrogeneDB ID: retro_hsap_3277

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:178349064..178349586(+)
• Located in intron of: ENSG00000198939

Retrocopy information

• Ensembl ID: ENSG00000253869
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PIGF
• Ensembl ID: ENSG00000151665
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class F [Source:HGNC Symbol;Acc:8962]

Sequence

>retro_hsap_3277
ATGAAAGATACCGATATCAAGAGACTACTGTATACCCATCTTTTATGCATATTTTCAATTATCCTAAGTGTCTTCATTCC
ATCACTCTTCTTGGAGAACTCCTCAATATTGGAAACACACTTGACATGGTTGTGCGTCTGTTCTGGTTTTGTAACTGCTG
TCAGTCTAGTACTATATTTAGTAGTGAAACCAAATACATCCTCTAAAATAAGTTCATTATCATACAAGGTAACCAGATTT
TTGAAATGCTGTATCTACTTTCTTATGTCTTGTTTCTCCTTTCATGTAATTTTTGTTCTATATGGAGCACCACTAATAGA
GTTGGCATTGGAAACATTTTTATTTGCAGTTATTTTGTCTACTTTTACTATTGTGCCTTACTTATGTTTGTTAGGACCAA
ACCTCAAAGCATGGCTAAGAGTTTTCAGTAGAAATGGAGTTACATCCATATGGGAGAATAGTCTCCAGATCACTGCAATG
TCTAGTTTTGTAGGAGCATGGCTTGGAGCACGTCCTATTCCT

Alignment

ORF - retro_hsap_3277 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 84.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKDNDIKRLLYTHLLCIFSIILSVFIPSLFLENFSILETHLTWLCICSGFVTAVNLVLYLVVKPNTSSKR
          MKD.DIKRLLYTHLLCIFSIILSVFIPSLFLEN.SILETHLTWLC.CSGFVTAV.LVLYLVVKPNTSSK.
Retrocopy MKDTDIKRLLYTHLLCIFSIILSVFIPSLFLENSSILETHLTWLCVCSGFVTAVSLVLYLVVKPNTSSKI

Parental  SSLSHKVTGFLKCCIYFLMSCFSFHVIFVLYGAPLIELALETFLFAVILSTFTTVPCLCLLGPNLKAWLR
          SSLS.KVT.FLKCCIYFLMSCFSFHVIFVLYGAPLIELALETFLFAVILSTFT.VP.LCLLGPNLKAWLR
Retrocopy SSLSYKVTRFLKCCIYFLMSCFSFHVIFVLYGAPLIELALETFLFAVILSTFTIVPYLCLLGPNLKAWLR

Parental  VFSRNGVTSIWENSLQITTISSFVGAWLGALPIP
          VFSRNGVTSIWENSLQIT..SSFVGAWLGA.PIP
Retrocopy VFSRNGVTSIWENSLQITAMSSFVGAWLGARPIP

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	4.11 RPM
bodymap2_adrenal	0.00 RPM	5.38 RPM
bodymap2_brain	0.02 RPM	5.18 RPM
bodymap2_breast	0.04 RPM	8.19 RPM
bodymap2_colon	0.00 RPM	6.26 RPM
bodymap2_heart	0.00 RPM	4.67 RPM
bodymap2_kidney	0.10 RPM	12.47 RPM
bodymap2_liver	0.00 RPM	4.14 RPM
bodymap2_lung	0.00 RPM	6.28 RPM
bodymap2_lymph_node	0.00 RPM	10.73 RPM
bodymap2_ovary	0.02 RPM	9.85 RPM
bodymap2_prostate	0.00 RPM	7.34 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.86 RPM
bodymap2_testis	0.00 RPM	12.61 RPM
bodymap2_thyroid	0.00 RPM	5.72 RPM
bodymap2_white_blood_cells	0.00 RPM	8.80 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3277 was not detected

EST

No EST(s) were mapped for retro_hsap_3277 retrocopy.

TSS

No TSS is located nearby retro_hsap_3277 retrocopy 5' end.

Lab

retro_hsap_3277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3277 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028483	1 retrocopy	retro_acar_103,
Callithrix jacchus	ENSCJAG00000000680	2 retrocopies	retro_cjac_4146, retro_cjac_481,
Dasypus novemcinctus	ENSDNOG00000007278	2 retrocopies	retro_dnov_1980, retro_dnov_502,
Dasypus novemcinctus	ENSDNOG00000025474	1 retrocopy	retro_dnov_602,
Dipodomys ordii	ENSDORG00000006083	1 retrocopy	retro_dord_234,
Homo sapiens	ENSG00000151665	3 retrocopies	retro_hsap_3277 , retro_hsap_4217, retro_hsap_4801,
Gorilla gorilla	ENSGGOG00000024478	3 retrocopies	retro_ggor_2229, retro_ggor_2825, retro_ggor_2988,
Myotis lucifugus	ENSMLUG00000008686	1 retrocopy	retro_mluc_1471,
Macaca mulatta	ENSMMUG00000005389	2 retrocopies	retro_mmul_1173, retro_mmul_2559,
Monodelphis domestica	ENSMODG00000000968	1 retrocopy	retro_mdom_1771,
Mustela putorius furo	ENSMPUG00000012037	1 retrocopy	retro_mputfur_810,
Nomascus leucogenys	ENSNLEG00000016924	3 retrocopies	retro_nleu_1115, retro_nleu_1455, retro_nleu_2882,
Oryctolagus cuniculus	ENSOCUG00000001130	1 retrocopy	retro_ocun_618,
Otolemur garnettii	ENSOGAG00000026734	1 retrocopy	retro_ogar_1699,
Pongo abelii	ENSPPYG00000012438	3 retrocopies	retro_pabe_2710, retro_pabe_3450, retro_pabe_3733,
Pan troglodytes	ENSPTRG00000011895	2 retrocopies	retro_ptro_2863, retro_ptro_3192,
Ictidomys tridecemlineatus	ENSSTOG00000001373	1 retrocopy	retro_itri_989,
Tupaia belangeri	ENSTBEG00000000891	1 retrocopy	retro_tbel_3809,
Tarsius syrichta	ENSTSYG00000002842	3 retrocopies	retro_tsyr_1497, retro_tsyr_1556, retro_tsyr_1820,
Vicugna pacos	ENSVPAG00000000314	1 retrocopy	retro_vpac_478,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 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	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 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	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

The presence of retro_hsap_3277 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_3277 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	5:178348361..178353000	97.54	97.16	97.94	97.73	86.36	90	90	89.29	89.33	86.02	86.22	100	100	100

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Indel #1, located at the genomic coordinates 5:178348361..178353000.