RetrogeneDB ID: retro_pabe_3112

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:157459941..157461167(+)
• 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_3112
ATCAAGAGACCCATGGCGTCTGAGGTGCCTTGTGCCTCGGGCATGCCAATCAAGAAAACAGGCCATCGAGGTGTTGGTTC
CTCAGGAGAGACAACCTATAGAAAGACGACCTCATCAGCCTTGAAATGTGCCATCCAGTTGGGCATTACTCACACTGTGG
GGAGCCTGGGTCCCACACCAGAGCGTGATGTCCTCATGCAAGATTTCTGCGTGGTGGAGAGTATCTTCTTCCCCAGTGGA
GGGAGCAACCTGACCCCTGCTCATCACTGCAGTGACTTTCCTTTCAAGACCTATACACCTATTGTCTTCTGCTACTTTCA
GGAGCTATTTGGTATCTGCCCTGTTGATGACTTGTACTCCCTCTGCAGTAAGCCACTGATTGAACTCAGTAGCTCTGGAG
CTGATGGGTTCCCTATTATATGTGTCCATCCACGATGAATTCATTATTAAAACAGTCCAACATAAAGAGGCGGAGTTTCT
GCAGAAGCTGCTTCCAGGATACCACATCGGACCTCAACCAGAACCCTTGGACTTTGCTGCCTAAATTCTGTGGACTGTGC
TGTGTGCTGGCAGGCAGCAAGAACATGCGGATTGTGGTGATGAAGAATCTCTTACTAAGACTGGTCAAAATGCATACCAA
ATATGACTTCAAAGGTTCAACCTACAAAAAGCAGGCTTCCCAGAAAGAGCAAGAGAAGCCTCTTCCCACATTTAAAAACC
TAGACTTCTTACAAGACATCCCGATGGTCTTTTTTTGGATGCTGACATGTACAGTGCTCTCTGTAAGACCCTGCAGCATG
ACTGTTTGGTGCTGCAGATCTTTGAGATAATGGACTATAGCCTCTTGATATCAATCCACAACATAGATCATGCACGAGAG
CCCTTAAGCAGCCAAACACAATGCTCAGTTCACACTTGAAGACCAGACCCCACAAAGGGCTCTGTATTCCACAGCCATGG
AATCCATCCAGGGAGAGGCTTGATGGGGCAGCCTCATGGAGACTGATGACCATACGGGTGGCATCCCTGCCCAGAATAGT
AGAGGGGAGAGGATCTTGCTTTGTATTGGCATCACTGACATTCTGCAGTCTTACAGGTTTGTTAAGAAGCTGGAGCATTC
TCGGAAAGCCCTGGTATGTGATGGGGACACAGTCTCAGTGCATCCCCCAGGCTTCTACACTGAACGGTTCCAGTGCTTCA
TGTGCAACACAGCATTTAAGAAGATC

Alignment

ORF - retro_pabe_3112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.11 %
• Parental protein coverage: 74.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IKRPMASEVPYASGMPIKKIGHRSVDSSGETTYKKTTSSALKGAIQLGITHTVGSLSTKPERDVLMQDFY
          IKRPMASEVP.ASGMPIKK.GHR.V.SSGETTY.KTTSSALK.AIQLGITHTVGSL...PERDVLMQDF.
Retrocopy IKRPMASEVPCASGMPIKKTGHRGVGSSGETTYRKTTSSALKCAIQLGITHTVGSLGPTPERDVLMQDFC

Parental  VVESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFRYFRELFGIRPDDYLYSLCSEPLIELCSSGAS-GSLF
          VVESIFFPS.GSNLTPAHH..DF.FKTY.P..F.YF.ELFGI.P.D.LYSLCS.PLIEL.SSGA..GSL.
Retrocopy VVESIFFPSGGSNLTPAHHCSDFPFKTYTPIVFCYFQELFGICPVDDLYSLCSKPLIELSSSGAD>GSLL

Parental  YVSSDDEFIIKTVQHKEAEFLQKLLPGYYM-NLNQNPRTLLPKFYGLYCVQAGGKNIRIVVMNNLLPRSV
          YVS..DEFIIKTVQHKEAEFLQKLLPGY....LNQNP.TLLPKF.GL.CV.AG.KN.RIVVM.NLL.R.V
Retrocopy YVSIHDEFIIKTVQHKEAEFLQKLLPGYHI>DLNQNPWTLLPKFCGLCCVLAGSKNMRIVVMKNLLLRLV

Parental  KMHIKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDI-PDGLFLDADMYNALCKTLQRDCLVLQSFKIM
          KMH.KYD.KGSTYK..ASQKE.EKPLPTFK.LDFLQDI.PDGLFLDADMY.ALCKTLQ.DCLVLQ.F.IM
Retrocopy KMHTKYDFKGSTYKKQASQKEQEKPLPTFKNLDFLQDI<PDGLFLDADMYSALCKTLQHDCLVLQIFEIM

Parental  DYSLLMSIHNIDHAQREPLSSETQYSVDTRRP-APQKALYSTAMESIQGEARRGGTMETDDHMGGIPARN
          DYSLL.SIHNIDHA.REPLSS.TQ.SV.T.RP..PQ.ALYSTAMESIQGEA..G..METDDH.GGIPA.N
Retrocopy DYSLLISIHNIDHA-REPLSSQTQCSVHT*RP>TPQRALYSTAMESIQGEA*WGSLMETDDHTGGIPAQN

Parental  SKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDGDTVSVHRPGFYAERFQRFMCNTVFKKI
          S.GER.LL.IGI.DILQSYRFVKKLEHS.KALV.DGDTVSVH.PGFY.ERFQ.FMCNT.FKKI
Retrocopy SRGERILLCIGITDILQSYRFVKKLEHSRKALVCDGDTVSVHPPGFYTERFQCFMCNTAFKKI

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	0.00 RPM	29.97 RPM
SRP007412_cerebellum	0.00 RPM	28.33 RPM
SRP007412_heart	0.00 RPM	17.16 RPM
SRP007412_kidney	0.00 RPM	21.91 RPM
SRP007412_liver	0.00 RPM	17.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3112 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3112 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2566

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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,