RetrogeneDB ID: retro_ptro_511

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:93517553..93518957(-)
• Located in intron of: None

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_511
ACAACCTCATCAGCCTTGAAAGGTGCCATCCAGTTAGGCATTACCCACACTGTGGGGAGCCTGAGTACCAAACCAGAGAG
TGATGTCCTCATGCAAGATTTCCACATGGTGGAGAGTATCTTCTTTCCCAGTGAAGGGAGCAACCTGACCCCTGCTCATC
ACTACAATGCCTTTCGTTTCAAGACCTATGCACCTGTTGCCTTCCGCTACTTCTGGGAGCTATTTGGTATCCGGCCCAGT
GATTACTTGTATTCCCTCTGCAGTGAGCCGCTGATTGAACTCTGTAGCTCTGGAGCTAGTGGTTCCCTGTTCTATGTGTC
CAGCGACGATGAGTTCATTATTAAGACAGTCCGACATAAAGAGGCGGAGTTTCTGCAGAAGCTGCTTCCAGGATACTACA
TAAACCTCAACCAGAACCCTCGGACTTTGCTGCCTAAATTCTATGGACTGTACTGTGTGCAGGCAGGTGGCAAGAACATT
CGGATTGTGGTGATGAACAATCTTTTACCAAGATCGGTAAAAATGCATATCAAATATGACCTCAAAGGCTCAACCTACAG
ACGGCGGGCTTCCCAGAAAGAGCGAGAGAAGCCTCTTCCCACATTTAAAGACCTAGACTTCTTACAAGACATCCCTGATG
GTCTTTTTTTGGATGCTGACGTGCACAACGCTCTCTGTAAGACCCTGCAGCGTGACTGTTTGGTGCTGCAGAGCTTCAAG
ATAATGGATTATAGCCTCTTGATGTCAATCCATAATATAGATCATGCACAACGAGAGCCCTTAAGCAGCGAAACACAATA
CTCAGTTGATACTCAAAGACCGGCCCCCCAAAAGGCTCCGTATTCCACAGCCATGGAATCCATCCAGGGAGAGGCTCGAC
GGGGTGGCACCATGGAGACTGACGACCATATGGGTGGCATCCCTGCCCGGAATAGTAAAGGGGAAAGGCTTCTGCTTTAT
ATTGGCATCATTGACATTCTACAGTCTTACAGGTTTGTTAAGAAGTTGGAGCACTCTTGGAAAGCCCTGGTACATGACAG
AGACACTGTCTCAGTGCATCGCCCAGGCTTCTATGCTGAATGGTTCCAGCGCTTCATGTGCAACACGGTATTTAAGAAGA
TTCCCTTGAAGCCTTCTCCTTCCAAAAAACTTCAGTCTGGCTCATCTTTCTCTCAGCGAGCAGGCTCCAGTGGCAACTCC
TGCATTACTTACCAGCCATTGGTCTCTGGGGAACACAAGGCACAAGTGACAACAAAGGCGGAAGTGGAGCCAGGCGTTCA
CCTTGGTCGTCCTGATGTTTTACCTCAGACTCCACCTTTGGAGGAAATCAGTGAGGGCTCACCTATTCCTGACCCCAGTT
TCTCACCTGTAGTTGGAGAGACTTTGCAAACGCTAACTACAAGT

Alignment

ORF - retro_ptro_511 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.51 %
• Parental protein coverage: 85.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTSSALKGAIQLGITHTVGSLSTKPERDVLMQDFYVVESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFRY
          TTSSALKGAIQLGITHTVGSLSTKPE.DVLMQDF..VESIFFPSEGSNLTPAHHYN.FRFKTYAPVAFRY
Retrocopy TTSSALKGAIQLGITHTVGSLSTKPESDVLMQDFHMVESIFFPSEGSNLTPAHHYNAFRFKTYAPVAFRY

Parental  FRELFGIRPDDYLYSLCSEPLIELCSSGASGSLFYVSSDDEFIIKTVQHKEAEFLQKLLPGYYMNLNQNP
          F.ELFGIRP.DYLYSLCSEPLIELCSSGASGSLFYVSSDDEFIIKTV.HKEAEFLQKLLPGYY.NLNQNP
Retrocopy FWELFGIRPSDYLYSLCSEPLIELCSSGASGSLFYVSSDDEFIIKTVRHKEAEFLQKLLPGYYINLNQNP

Parental  RTLLPKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQD
          RTLLPKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDLKGSTY.RRASQKEREKPLPTFKDLDFLQD
Retrocopy RTLLPKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDLKGSTYRRRASQKEREKPLPTFKDLDFLQD

Parental  IPDGLFLDADMYNALCKTLQRDCLVLQSFKIMDYSLLMSIHNIDHAQREPLSSETQYSVDTRRPAPQKAL
          IPDGLFLDAD..NALCKTLQRDCLVLQSFKIMDYSLLMSIHNIDHAQREPLSSETQYSVDT.RPAPQKA.
Retrocopy IPDGLFLDADVHNALCKTLQRDCLVLQSFKIMDYSLLMSIHNIDHAQREPLSSETQYSVDTQRPAPQKAP

Parental  YSTAMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDGDTV
          YSTAMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHD.DTV
Retrocopy YSTAMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDRDTV

Parental  SVHRPGFYAERFQRFMCNTVFKKIPLKPSPSKKFRSGSSFSRRAGSSGNSCITYQPSVSGEHKAQVTTKA
          SVHRPGFYAE.FQRFMCNTVFKKIPLKPSPSKK..SGSSFS.RAGSSGNSCITYQP.VSGEHKAQVTTKA
Retrocopy SVHRPGFYAEWFQRFMCNTVFKKIPLKPSPSKKLQSGSSFSQRAGSSGNSCITYQPLVSGEHKAQVTTKA

Parental  EVEPGVHLGRPDVLPQTPPLEEISEGSPIPDPSFSPLVGETLQMLTTS
          EVEPGVHLGRPDVLPQTPPLEEISEGSPIPDPSFSP.VGETLQ.LTTS
Retrocopy EVEPGVHLGRPDVLPQTPPLEEISEGSPIPDPSFSPVVGETLQTLTTS

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	0.13 RPM	24.97 RPM
SRP007412_cerebellum	0.14 RPM	35.35 RPM
SRP007412_heart	0.00 RPM	13.84 RPM
SRP007412_kidney	0.08 RPM	29.66 RPM
SRP007412_liver	0.03 RPM	16.43 RPM
SRP007412_testis	74.08 RPM	63.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_511 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_511 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_716
Gorilla gorilla	retro_ggor_606
Pongo abelii	retro_pabe_619

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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 ,