RetrogeneDB ID: retro_hsap_1050

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:100972521..100973972(+)
• Located in intron of: ENSG00000139354

Retrocopy information

• Ensembl ID: ENSG00000257803
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PIGA
• Ensembl ID: ENSG00000165195
• Aliases: PIGA, GPI3, MCAHS2, PIG-A
• Description: phosphatidylinositol glycan anchor biosynthesis, class A [Source:HGNC Symbol;Acc:8957]

Sequence

>retro_hsap_1050
ATGGCGTATAAAGGAGAAGGTGGGCATGGCCAGCCTCCCTCAGCTACACTGTCTCAGGTTAGCCCTGGAAGTCTTTACAC
ACGTAGAACCCATACCCATAATATATGTATGGCATCTGACTTTTTCTACCCAAATATGGGAGGTGTGGAAAGCCACATTT
ACCAGCTCCCTCAGTGCCTGATTGGAAGAGGGGATAAGGTTATAATTGTCATCCATGCTTATGGAAATCGAAAAGGCATC
CGTTACCTCACTAATGACCTCAAAGTCTATTACTTGCCTCTGAAAGTCATGTATAACCAGTCTATGGCCATGACCCTCTT
TCACAGTCTGCCATTGCTCAAGTACATATTTGTTCAGGAGAGAGTCACAATAATCCATTCACATAGTTCATTTTCTGCCA
TGGCCCATGATGTTCTCTTCCATGCCAAGACAATGGGGCTTCAAACAGTCTTAACAGACCATCCCCTTTCTGGATTTGCT
AAGGTCCATTCAGTGCTTACAAACAAACTTCTAACTGTGTCTCTTTGTGACACAAGCCGTATCATTTGCGTTTCTTATAC
TAGTAAGGAAAATACCGTACTACGAGCGGCACTGATTACTGAAATAGTGTCTGTCATTCCTAACGCTGTAGATCCTATTG
ACTTCACTCCAGACCCATTTAGAAGGCATGATAGTATAACTATTGTTGTCAGCAGACTTGTTTACAGAAAGGGAACAAAT
TTGGTTAGTGGTATTATACCCAAACTCTTGTCAGAAATATTAAGATTTAAATTTCATAATTGGAGGAGAGGGACCAAAGA
GAATCATTTTGCAAGAAGTTCCGGAAAGATACCAGTTGCATGACAGGGTGCATCTTTTGGGAGCTTTAGAACACAAGAAT
GTTAGAAATGTCTTAGTTCAAGGACATATTTTTCTTAATACCTCCCTTACTGAAGCATTCTGCATGGCGATCATGGAAGC
AGCCAGCTGTGGTTTACAGGTTGTAAGTACCAGGGTTGGTGGAATTCCTGAGGTGCTTCCGGAAAATCTTACTATTTTAT
GAGAAACTTCAGTAAAATCTTTGTGTGAGGGATTGGAAAAAGCTATTTTCCAACTGAAGTCAGGGGCATTGCTGGCTCCA
GAAAATATCCGTAACATAGTAAAGACTTTCCACACCTGAAGGAATGTTGTGGAGAGAACTGAAAAAGCGTATGACCAAGT
ATCAGTGGAATCTGTGTTGCCAATGGACAAACAACTGGACAGACTTATTTCTCACAGTGGACCAGTAACAGGCTACATCT
TTGCTTTGTTGGCTGTTTTCAACTTCCTCTTCCTCATTTTCTTGAGATGGATGACTCCAGATTCTTATCATTGATACTGG
AATAGATGCCACTGGGCCAAGGGGTGCCTGGACTCATAAATGTTCTCACAGTAAAAGAGGGGGTGAGAATATTAAGATAT
CTAAAACCAGG

Alignment

ORF - retro_hsap_1050 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MACRGGAGNGHRASATLSRVSPGSLYTCRTRTHNICMVSDFFYPNMGGVESHIYQLSQCLIERGHKVIIV
          MA..G..G.G...SATLS.VSPGSLYT.RT.THNICM.SDFFYPNMGGVESHIYQL.QCLI.RG.KVIIV
Retrocopy MAYKGEGGHGQPPSATLSQVSPGSLYTRRTHTHNICMASDFFYPNMGGVESHIYQLPQCLIGRGDKVIIV

Parental  THAYGNRKGIRYLTSGLKVYYLPLKVMYNQSTATTLFHSLPLLRYIFVRERVTIIHSHSSFSAMAHDALF
          .HAYGNRKGIRYLT..LKVYYLPLKVMYNQS.A.TLFHSLPLL.YIFV.ERVTIIHSHSSFSAMAHD.LF
Retrocopy IHAYGNRKGIRYLTNDLKVYYLPLKVMYNQSMAMTLFHSLPLLKYIFVQERVTIIHSHSSFSAMAHDVLF

Parental  HAKTMGLQTVFTDHSLFGFADVSSVLTNKLLTVSLCDTNHIICVSYTSKENTVLRAALNPEIVSVIPNAV
          HAKTMGLQTV.TDH.L.GFA.V.SVLTNKLLTVSLCDT..IICVSYTSKENTVLRAAL..EIVSVIPNAV
Retrocopy HAKTMGLQTVLTDHPLSGFAKVHSVLTNKLLTVSLCDTSRIICVSYTSKENTVLRAALITEIVSVIPNAV

Parental  DPTDFTPDPFRRHDSITIVVVSRLVYRKGIDLLSGIIPEL-CQKYPDLNFIIGGEGPKRIILEEVRERYQ
          DP.DFTPDPFRRHDSITI.VVSRLVYRKG..L.SGIIP.L.CQKY.DLNFIIGGEGPKRIIL.EV.ERYQ
Retrocopy DPIDFTPDPFRRHDSITI-VVSRLVYRKGTNLVSGIIPKL>CQKY*DLNFIIGGEGPKRIILQEVPERYQ

Parental  LHDRVRLLGALEHKDVRNVLVQGHIFLNTSLTEAFCMAIVEAASCGLQVVSTRVGGIPEVLPENLIILCE
          LHDRV.LLGALEHK.VRNVLVQGHIFLNTSLTEAFCMAI.EAASCGLQVVSTRVGGIPEVLPENL.IL.E
Retrocopy LHDRVHLLGALEHKNVRNVLVQGHIFLNTSLTEAFCMAIMEAASCGLQVVSTRVGGIPEVLPENLTIL*E

Parental  PSVKSLCEGLEKAIFQLKSGTLPAPENIHNIVKTFYTWRNVAERTEKVYDRVSVEAVLPMDKRLDRLISH
          .SVKSLCEGLEKAIFQLKSG.L.APENI.NIVKTF.T.RNV.ERTEK.YD.VSVE.VLPMDK.LDRLISH
Retrocopy TSVKSLCEGLEKAIFQLKSGALLAPENIRNIVKTFHT*RNVVERTEKAYDQVSVESVLPMDKQLDRLISH

Parental  CGPVTGYIFALLAVFNFLFLIFLRWMTPDS-IIDVAIDATGPRGAWTNNYSHSKRGGENNEISETR
          .GPVTGYIFALLAVFNFLFLIFLRWMTPDS.IID..IDATGPRGAWT...SHSKRGGEN..IS.TR
Retrocopy SGPVTGYIFALLAVFNFLFLIFLRWMTPDS>IIDTGIDATGPRGAWTHKCSHSKRGGENIKISKTR

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	10.69 RPM
bodymap2_adrenal	0.12 RPM	10.58 RPM
bodymap2_brain	0.05 RPM	24.52 RPM
bodymap2_breast	0.04 RPM	10.78 RPM
bodymap2_colon	0.12 RPM	4.02 RPM
bodymap2_heart	0.00 RPM	5.59 RPM
bodymap2_kidney	0.08 RPM	16.32 RPM
bodymap2_liver	0.06 RPM	6.76 RPM
bodymap2_lung	0.00 RPM	35.21 RPM
bodymap2_lymph_node	0.16 RPM	11.46 RPM
bodymap2_ovary	0.00 RPM	10.68 RPM
bodymap2_prostate	0.00 RPM	12.90 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.11 RPM
bodymap2_testis	0.17 RPM	11.52 RPM
bodymap2_thyroid	0.00 RPM	14.18 RPM
bodymap2_white_blood_cells	0.00 RPM	10.77 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1050 was not detected

EST

No EST(s) were mapped for retro_hsap_1050 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_19975	321 libraries	321 libraries	1023 libraries	124 libraries	40 libraries

The graphical summary, for retro_hsap_1050 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_1050 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1050 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_716
Gorilla gorilla	retro_ggor_828
Pongo abelii	retro_pabe_876

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006415	1 retrocopy	retro_chof_2311,
Homo sapiens	ENSG00000165195	1 retrocopy	retro_hsap_1050 ,
Gorilla gorilla	ENSGGOG00000007293	1 retrocopy	retro_ggor_828,
Nomascus leucogenys	ENSNLEG00000009352	1 retrocopy	retro_nleu_2070,
Ochotona princeps	ENSOPRG00000015381	1 retrocopy	retro_opri_1065,
Pongo abelii	ENSPPYG00000020142	1 retrocopy	retro_pabe_876,
Pan troglodytes	ENSPTRG00000021684	1 retrocopy	retro_ptro_716,
Rattus norvegicus	ENSRNOG00000003554	1 retrocopy	retro_rnor_2566,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.24 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.19 RPM
FIN_HG00277	0.33 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.21 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.17 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.19 RPM
TSI_NA20771	0.11 RPM
TSI_NA20786	0.10 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.19 RPM
YRI_NA19214	0.05 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).