RetrogeneDB ID: retro_hsap_4245

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:33675440..33676646(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000237984
• Aliases: PTENP1, PTEN-rs, PTEN2, PTENpg1, PTH2, psiPTEN
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTEN
• Ensembl ID: ENSG00000171862
• Aliases: None
• Description: phosphatase and tensin homolog [Source:HGNC Symbol;Acc:9588]

Sequence

>retro_hsap_4245
ACAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTATAT
TTATCTAAACATTATTGCTATGGGATTTCCTGCAGAAAGACTTGAAGGCGTATACAGGAACAATATTGATGATGTAGTAA
GGTTTTTGGATTCAAAGCATAAAAACCATTACAAGATACACAATCTTTGTGCTGAAAGACATTATGACACCGCCAAATCT
AATTACAGAGTTGCGCAATATCCTTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCT
TGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTATAATGA
TTTATGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACCAGA
GACAAAAAGGGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTACTATAGCTACCTGGTAAAGAATCATGTGGATTA
TAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGT
TTGTGGTCTGCCAGCTAAAGGTGAAGATGTATTCCTCCAATTCAGGACCCACACGATGGGAGGACAAGTTCATGTATTTT
GAGTTCCCTCAGCCGTTACCTGTGTGTGGTGATATCAAAGTAGAGTTCTTCCACAAACAGAACAAGATGCTAAAAAAGGA
CAAAATGTTTCACTTTTGGGTAAATACATTCTTCATACCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGAAGTC
TATGTGATCAAGAAATTGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAGTATCTAGTACTTACTTTAACA
AAAAATGATCTTGACAAAGCAAATAAAGACAAAGCCAACCGATACTTTTCTCCAAATTTTAAGGTGAAGCTGTACTTCAC
AAAAACAGTAGAGGAGCCGTCAAATCCAGAGGCTAGCAGTTCAACTTCTGTAACACCAGATGTTAGTGACAATGAACCTG
ATCATTATAGATATTCTGACACCACTGACTCTGATCCAGAGAATGAACCTTTTGATGAAGATCAGCATACACAAATTACA
AAAGTC

Alignment

ORF - retro_hsap_4245 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.51 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLC
          TAIIKEIVSRNKRRYQEDGFDLDLTYIY.NIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKI.NLC
Retrocopy TAIIKEIVSRNKRRYQEDGFDLDLTYIYLNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIHNLC

Parental  AERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVMICAYLLH
          AERHYDTAK.N.RVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTG.MI.AYLLH
Retrocopy AERHYDTAKSNYRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGIMIYAYLLH

Parental  RGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFSGGTC
          RGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYL.KNH.DYRPVALLFHKMMFETIPMFSGGTC
Retrocopy RGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLVKNHVDYRPVALLFHKMMFETIPMFSGGTC

Parental  NPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIP
          NPQFVVCQLKVK.YSSNSGPTR.EDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIP
Retrocopy NPQFVVCQLKVKMYSSNSGPTRWEDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIP

Parental  GPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV
          GPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV
Retrocopy GPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV

Parental  EEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV
          EEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV
Retrocopy EEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV

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	2.88 RPM	263.62 RPM
bodymap2_adrenal	0.66 RPM	143.45 RPM
bodymap2_brain	1.69 RPM	118.84 RPM
bodymap2_breast	1.44 RPM	224.15 RPM
bodymap2_colon	2.07 RPM	233.87 RPM
bodymap2_heart	0.13 RPM	109.18 RPM
bodymap2_kidney	1.67 RPM	182.24 RPM
bodymap2_liver	0.36 RPM	76.59 RPM
bodymap2_lung	0.47 RPM	130.27 RPM
bodymap2_lymph_node	2.23 RPM	175.99 RPM
bodymap2_ovary	1.14 RPM	226.18 RPM
bodymap2_prostate	1.42 RPM	178.95 RPM
bodymap2_skeletal_muscle	0.36 RPM	93.43 RPM
bodymap2_testis	1.02 RPM	202.41 RPM
bodymap2_thyroid	1.60 RPM	182.19 RPM
bodymap2_white_blood_cells	3.52 RPM	382.02 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_4245 in 4 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	9:33677106..33677280
ENCFF002CFW	POLR2A	9:33676723..33676930
ENCFF002CFX	POLR2A	9:33676675..33676961
ENCFF002CFX	POLR2A	9:33677125..33677325
ENCFF002CJE	POLR2A	9:33677128..33677481
ENCFF002DAE	POLR2A	9:33676682..33676992

EST

No EST(s) were mapped for retro_hsap_4245 retrocopy.

TSS

No TSS is located nearby retro_hsap_4245 retrocopy 5' end.

Lab

retro_hsap_4245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4245 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009252	1 retrocopy	retro_chof_578,
Homo sapiens	ENSG00000171862	1 retrocopy	retro_hsap_4245 ,
Gorilla gorilla	ENSGGOG00000000893	1 retrocopy	retro_ggor_2846,
Nomascus leucogenys	ENSNLEG00000012141	1 retrocopy	retro_nleu_1280,
Pongo abelii	ENSPPYG00000002448	1 retrocopy	retro_pabe_3393,
Sarcophilus harrisii	ENSSHAG00000003709	1 retrocopy	retro_shar_828,
Sus scrofa	ENSSSCG00000010440	2 retrocopies	retro_sscr_236, retro_sscr_237,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.32 RPM
CEU_NA11843	0.11 RPM
CEU_NA11930	0.23 RPM
CEU_NA12004	0.23 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.29 RPM
CEU_NA12760	0.36 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.08 RPM
CEU_NA12873	0.32 RPM
FIN_HG00183	0.44 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.24 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.37 RPM
FIN_HG00375	0.46 RPM
FIN_HG00377	0.18 RPM
FIN_HG00378	0.19 RPM
GBR_HG00099	0.58 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.34 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.34 RPM
GBR_HG00133	0.24 RPM
GBR_HG00134	0.17 RPM
GBR_HG00137	0.33 RPM
GBR_HG00142	0.36 RPM
GBR_HG00143	0.26 RPM
TSI_NA20512	0.23 RPM
TSI_NA20513	0.27 RPM
TSI_NA20518	0.80 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.32 RPM
TSI_NA20756	0.52 RPM
TSI_NA20765	0.27 RPM
TSI_NA20771	0.40 RPM
TSI_NA20786	0.24 RPM
TSI_NA20798	0.16 RPM
YRI_NA18870	0.54 RPM
YRI_NA18907	0.17 RPM
YRI_NA18916	0.21 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.48 RPM
YRI_NA19114	0.18 RPM
YRI_NA19118	0.23 RPM
YRI_NA19213	0.38 RPM
YRI_NA19214	0.30 RPM
YRI_NA19223	0.14 RPM

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Indel association:

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