RetrogeneDB ID: retro_pabe_3393

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:27984780..27985784(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000019132
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTEN
• Ensembl ID: ENSPPYG00000002448
• Aliases: None
• Description: phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN [Source:RefSeq peptide;Acc:NP_001124955]

Sequence

>retro_pabe_3393
TATACGATCTTTGTGCTGAGACATTATGACACCGCCAAATTTAATTGCAGAGTTGCACAATATCCTTTTGAAGACCATAA
CCCACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAG
CAATTCACTGTAAAGCTGGAAAGGGATGAACTGGTGTAATGATTTATGCATATTTATTACATCGGGGCAAATTTTTAAAG
GCACAAGAGGCCGTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGGAGTAACTATTCCCAGTCAGAGGCGCTA
TGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTG
AAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTAAAGGTGAAGATATATTCCTCC
AATTCAGTACCCACACGACAGGAAGACAAGTTCATGTACTTTGAGTTCCCTCAGCCATTACCTGTGTGTGGTGATATCAA
AGTAGAGTTCTTCCACAAACAGAACAAGATGCTAAAAAAGGACAAAATGTTTCACTTTTGGGTAAATACGTTCTTCCTAC
CAGGACCAGAGGAAACTTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATTGATAGCATTTGCAGTATAGAG
CGTGCAGATAATGACAAGGAATATCTAGTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACAAAGCCAACCGA
TGCTTTTCTCCAGATTTTAAGGTGAAGCTGTACTTCACAAAAACAGTAGAGGAACCGTCAAATCCAGAAGCTAGCAGTTC
AACTTCTGTAACACCAGATGTTAGTGACAATGAACCTGATCATTATAGATATTCTGACACCACTGACTCTGATCCAGAGA
ATGAACCTTTTGATGAAGATCAGCATATACAAATTACAAAAGTC

Alignment

ORF - retro_pabe_3393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.58 %
• Parental protein coverage: 83.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVMICA
          Y.....RHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKG.TGVMI.A
Retrocopy YTIFVLRHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKG*TGVMIYA

Parental  YLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFS
          YLLHRGKFLKAQEA.DFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFS
Retrocopy YLLHRGKFLKAQEAVDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFS

Parental  GGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNT
          GGTCNPQFVVCQLKVKIYSSNS.PTR.EDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNT
Retrocopy GGTCNPQFVVCQLKVKIYSSNSVPTRQEDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNT

Parental  FFIPGPEETSEKVENGSLCDQEIDSICSIERADNDKEYQVLTLTKNDLDKANKDK-ANRYFSPNFKVKLY
          FF.PGPEETSEKVENGSLCDQEIDSICSIERADNDKEY.VL...K..L.K..K.K.ANR.FSP.FKVKLY
Retrocopy FFLPGPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVL-*QKMILTKQIKTK<ANRCFSPDFKVKLY

Parental  FTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV
          FTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQH.QITKV
Retrocopy FTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHIQITKV

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
SRP007412_brain_prefrontal_cortex	0.22 RPM	43.51 RPM
SRP007412_cerebellum	0.00 RPM	115.89 RPM
SRP007412_heart	0.03 RPM	21.76 RPM
SRP007412_kidney	0.07 RPM	30.06 RPM
SRP007412_liver	0.00 RPM	48.32 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3393 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3393 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,