RetrogeneDB ID: retro_pabe_3037

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6_random:3825803..3826787(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PIP5K1A
• Ensembl ID: ENSPPYG00000000872
• Aliases: None
• Description: phosphatidylinositol-4-phosphate 5-kinase, type I, alpha [Source:HGNC Symbol;Acc:8994]

Sequence

>retro_pabe_3037
GGCAAGAACATTCGGATTGTGGTGATGAACAATCTTTTACCAAGATCCGTCAAAATGCATATCAAATATGACCTCAAAGG
CTCAACCTACAAACGGCCAGGCTTCCCAGAAAGAGCGAGAGAAGCCTCTTCCCACATTTAAAGATCTAGACTTCTTACAA
GACATCCCTGATGGTCTTTTTTTGGATGCTGACATGTACAATGCTCTCTGTAAGACGGTGCAGCGTGACTGTTTGGTGCT
GCAGAGCTTCAAGATAATGGACTATAGCCTCTTGCTGTCAATCCACAATATAGATCATGCACAAGGAGAGCCCTTAAGCA
GCGACACTCTTCAAGTGTCAGTTGACACTCAAAGACTGGCCCCCCAAAAGGCTCTGTATTCCACAGCCATGGAATCCATC
CAGGGAGAGGCTCGACTGGGCGACACCATGGAGACCGATGACCATATGGGTGGCATCCCTGCTCAGAATAGTAAAGGGGA
AAGGCTTCTGCTTTATATTGGCATCATTGACATTCTACAGTCTTACACATTTCTTAAGAAGTTGGAGCACTCTTGGAAAG
CCGTGGTACATGACGGGGACACTGTTTCAGTGCATCGCCCAGGCTTCTATGCTGAACGGTTCCAGCGCTTCATGTGCAAT
GCAGTATTTAAGAAGATCCCCTTGAAGCCTTCTCCTTCCAAAAAGTTTCGGTCTGGCTTATCTTTCTCTCCGCAAACGGG
CTCCAGTGGCAACTCCTGCATTACTTACCAGCCATTGGTCTCTGGGGAACACAAGTCACAAGTGATAACAAAGGTGCAAG
TGGAGCCAGGTGTTCACCTTGGTCGTCCTGATGTTTTACCTCAGAATCCACCTTTGGAGGAAATCAGTGAGGGCTACCTA
TTACTGACCACAGTTTCTCACCTGTAGTTGGAAAGACTTTGCATATGCTAACTACAAGTACAACCTTGGAAAAGCTTGAA
TGTACAGAGTCAGAGTTCACCCAT

Alignment

ORF - retro_pabe_3037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.09 %
• Parental protein coverage: 59.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKR-RASQKEREKPLPTFKDLDFLQDIPDGLFLDADMYNAL
          GKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKR..ASQKEREKPLPTFKDLDFLQDIPDGLFLDADMYNAL
Retrocopy GKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKR>QASQKEREKPLPTFKDLDFLQDIPDGLFLDADMYNAL

Parental  CKTLQRDCLVLQSFKIMDYSLLMSIHNIDHAQREPLSSET-QYSVDTRRPAPQKALYSTAMESIQGEARR
          CKT.QRDCLVLQSFKIMDYSLL.SIHNIDHAQ.EPLSS.T.Q.SVDT.R.APQKALYSTAMESIQGEAR.
Retrocopy CKTVQRDCLVLQSFKIMDYSLLLSIHNIDHAQGEPLSSDTLQVSVDTQRLAPQKALYSTAMESIQGEARL

Parental  GGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDGDTVSVHRPGFYAERFQR
          G.TMETDDHMGGIPA.NSKGERLLLYIGIIDILQSY.F.KKLEHSWKA.VHDGDTVSVHRPGFYAERFQR
Retrocopy GDTMETDDHMGGIPAQNSKGERLLLYIGIIDILQSYTFLKKLEHSWKAVVHDGDTVSVHRPGFYAERFQR

Parental  FMCNTVFKKIPLKPSPSKKFRSGSSFSRRAGSSGNSCITYQPSVSGEHKAQVTTKAEVEPGVHLGRPDVL
          FMCN.VFKKIPLKPSPSKKFRSG.SFS...GSSGNSCITYQP.VSGEHK.QV.TK..VEPGVHLGRPDVL
Retrocopy FMCNAVFKKIPLKPSPSKKFRSGLSFSPQTGSSGNSCITYQPLVSGEHKSQVITKVQVEPGVHLGRPDVL

Parental  PQTPPLEEISE-GSPIPDPSFSPLVGETLQMLTTSTTLEKLEVAESEFTH
          PQ.PPLEEISE.G.PI.D.SFSP.VG.TL.MLTTSTTLEKLE..ESEFTH
Retrocopy PQNPPLEEISE<GLPITDHSFSPVVGKTLHMLTTSTTLEKLECTESEFTH

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	0.06 RPM	29.97 RPM
SRP007412_cerebellum	0.12 RPM	28.33 RPM
SRP007412_heart	0.00 RPM	17.16 RPM
SRP007412_kidney	0.03 RPM	21.91 RPM
SRP007412_liver	0.03 RPM	17.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3037 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3037 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3037 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000143398	2 retrocopies	retro_hsap_3420, retro_hsap_716,
Macaca mulatta	ENSMMUG00000005228	1 retrocopy	retro_mmul_1748,
Nomascus leucogenys	ENSNLEG00000010130	2 retrocopies	retro_nleu_468, retro_nleu_5,
Otolemur garnettii	ENSOGAG00000002846	1 retrocopy	retro_ogar_1855,
Pongo abelii	ENSPPYG00000000872	4 retrocopies	retro_pabe_3037 , retro_pabe_3112, retro_pabe_59, retro_pabe_619,
Pan troglodytes	ENSPTRG00000001282	2 retrocopies	retro_ptro_2324, retro_ptro_511,