RetrogeneDB ID: retro_ptro_2324

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:8044883..8046529(+)
• Located in intron of: ENSPTRG00000017708

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIP5K1A
• Ensembl ID: ENSPTRG00000001282
• Aliases: None
• Description: Pan troglodytes phosphatidylinositol-4-phosphate 5-kinase, type I, alpha (PIP5K1A), mRNA. [Source:RefSeq mRNA;Acc:NM_001137558]

Sequence

>retro_ptro_2324
ATGGCGTCGGCCTCCTCCCAACCGTCGCTGGCGGTCGGTTTTTCATCCTTTGATCCCGGGGCCCCTTCCTGTACCGCGTC
CTCAGCATCTGGAATCATGAGCCCCACGGCATCTGAGGTGCCTTATGCCTCTGGCAGGCCCATCAAGAAAACAGGCCATC
GAAGTGTTGATTCCTCAGGAGAGACAACATATAAAAAGGCCTCAACGGCCTTGAAAGGTGCCATCCAGTTAGGCATTACT
TACACTGTGGGGAGCCTGAGTACCAAACCAGAGCGTGATGTCCTCATGCAAGATTTCTACGCGGTGGAGAGTATCTTCTT
CCCCAGTGAAGGGAGCAACCTGACCCCTGCTCATCACTACAATGACTTCCGTTTCAAGACCTATGCGCCTGTTGCCTTCC
GCTACTTTCGGGAGCTATTTGGTATCCCGCCCGATGATTACTTGTGCTCCCTCTGCGGTGAGCCGCTGATTGAACTCTGT
AGCTCTGGAGCTAGTGGTTCCCTGTTCTATGTGTCCAGCGACGATGAACTCATTATTAAGACACTCCAACATAAAGAGGC
GGAGTTTCTGCAGAAGCTGCTTCCAGGATACTACTTGAACCTCAGCCAGAACCCTCGGACTTTGCTGCCTAAATTCTTTG
GACTGTACTGTGTGCAGACAGGTGGCAAGAACATTCGGATTGTGGTGATGAACAATCTTTTACCAAGATCCGTCAAAATG
CATATCAAATATGACCTCAAAGGCTCAACCTACAAACGCCGGGCTTCCCAGAAAGAGCGAGAGAAGCCTCTTCCCACATT
TAAAGATCTAGACTTCTTACAAGACATCCCTGATGGTCTTTTTTTGGATGCTGACATGTACAATGCTCTCTGTAAGACCC
TGCAGCGTGACTGTTTGGTGCTGCAGAGCTTCAAGATAATGGACTATAGCCTCTGGCTGTCAATCCACAATATAGATCAT
GCACAACGAGAGCCCTTAAGCAGCGACACTCTTCAAGTGTCAATCGACACTCAAAGACTGGCTCCCCAAAAGGCTCTGTA
TTCCACAGCCATGGAATTCATCCAGGGAGAGGCTCGGCTGGGCGACACCATGGAGGCCGATGACCATATGGGTGGCATCC
CTGCTCAGAATAGTAAAGGGGAAAGGCTTCTGCTTTATATTGGCATCATTGACATTCTACAGTCTTACACGTTTCTTAAG
AAGTTGGAGCACTCTTGGAAAGCCGTGGTACATGACGGGGACGCTGTCTCAGTGCATCGCCCAGGCTTCTACGCTGAACG
GTTCCAGCACTTCATGTGCGACGCAGTATTTAAGAAGATCCCCTTGAAGCCTTCTCCTTCCAAAAAGTTTCGGTCTGGCT
TATCTTTCTCTCCGCATACGGGCTCCAGTGGCAACTCCTGCATTACTTACCAGCCATTGGTCTCTGAGGAACACAAGTCA
CAAGTGATAACAAAGGTGCAAGTGGAGCCAGGTGTTCACCTTGGTCGTTCTGATGTTTTACCTCAGAATCCACCTTTGGA
GGAAATCAGTGAGGGCTCACTATTACTGACCACAGTTTCTCACCTGTAGTTGGAAAGACTTTGCATATGCTAACTACAAG
TATAACCCTGGAAAAACTTGAATGTACAGAGTCAGAGTTCACCCAT

Alignment

ORF - retro_ptro_2324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASASSGPSSSVGFSSFDPAVPSCTSSSAASGIKRPMASEVPYASGMPIKKIGHRSVDSSGETTYKKTTS
          MASASS.PS..VGFSSFDP..PSCT.SSA.SGI..P.ASEVPYASG.PIKK.GHRSVDSSGETTYKK..S
Retrocopy MASASSQPSLAVGFSSFDPGAPSCTASSA-SGIMSPTASEVPYASGRPIKKTGHRSVDSSGETTYKKA-S

Parental  SALKGAIQLGITHTVGSLSTKPERDVLMQDFYVVESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFRYFRE
          .ALKGAIQLGIT.TVGSLSTKPERDVLMQDFY.VESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFRYFRE
Retrocopy TALKGAIQLGITYTVGSLSTKPERDVLMQDFYAVESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFRYFRE

Parental  LFGIRPDDYLYSLCSEPLIELCSSGASGSLFYVSSDDEFIIKTVQHKEAEFLQKLLPGYYMNLNQNPRTL
          LFGI.PDDYL.SLC.EPLIELCSSGASGSLFYVSSDDE.IIKT.QHKEAEFLQKLLPGYY.NL.QNPRTL
Retrocopy LFGIPPDDYLCSLCGEPLIELCSSGASGSLFYVSSDDELIIKTLQHKEAEFLQKLLPGYYLNLSQNPRTL

Parental  LPKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDIPD
          LPKF.GLYCVQ.GGKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDIPD
Retrocopy LPKFFGLYCVQTGGKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDIPD

Parental  GLFLDADMYNALCKTLQRDCLVLQSFKIMDYSLLMSIHNIDHAQREPLSSET-QYSVDTRRPAPQKALYS
          GLFLDADMYNALCKTLQRDCLVLQSFKIMDYSL..SIHNIDHAQREPLSS.T.Q.S.DT.R.APQKALYS
Retrocopy GLFLDADMYNALCKTLQRDCLVLQSFKIMDYSLWLSIHNIDHAQREPLSSDTLQVSIDTQRLAPQKALYS

Parental  TAMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDGDTVSV
          TAME.IQGEAR.G.TME.DDHMGGIPA.NSKGERLLLYIGIIDILQSY.F.KKLEHSWKA.VHDGD.VSV
Retrocopy TAMEFIQGEARLGDTMEADDHMGGIPAQNSKGERLLLYIGIIDILQSYTFLKKLEHSWKAVVHDGDAVSV

Parental  HRPGFYAERFQRFMCNTVFKKIPLKPSPSKKFRSGSSFSRRAGSSGNSCITYQPSVSGEHKAQVTTKAEV
          HRPGFYAERFQ.FMC..VFKKIPLKPSPSKKFRSG.SFS...GSSGNSCITYQP.VS.EHK.QV.TK..V
Retrocopy HRPGFYAERFQHFMCDAVFKKIPLKPSPSKKFRSGLSFSPHTGSSGNSCITYQPLVSEEHKSQVITKVQV

Parental  EPGVHLGRPDVLPQTPPLEEISEGS-PIPDPSFSPLVGETLQMLTTSTTLEKLEVAESEFTH
          EPGVHLGR.DVLPQ.PPLEEISEGS..I.D.SFSP.VG.TL.MLTTS.TLEKLE..ESEFTH
Retrocopy EPGVHLGRSDVLPQNPPLEEISEGS<TITDHSFSPVVGKTLHMLTTSITLEKLECTESEFTH

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	0.05 RPM	24.97 RPM
SRP007412_cerebellum	0.07 RPM	35.35 RPM
SRP007412_heart	0.00 RPM	13.84 RPM
SRP007412_kidney	0.05 RPM	29.66 RPM
SRP007412_liver	0.10 RPM	16.43 RPM
SRP007412_testis	26.35 RPM	63.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2324 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2324 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2324 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3420
Macaca mulatta	retro_mmul_1748

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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,