RetrogeneDB ID: retro_pabe_619

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:92736101..92737507(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000002498
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_619
GAGACAACCTCATCAGCCTTGAAAGGTGCCATCCAGTTAGGCATTACCCACACTGTGGGGAGCCTGAGTACCAGACCAGA
GAGTGATGTCCTCATGCAAGATTTCCACATGGTGGAGAGTATCTTCTTTCCCAGTGAAGGGAGCAACCTGACCCCTGCTC
ATCACTACAATGACTTTCGTTTCAAGACCTATGCACCTGTTGCCTTCCGCTACTTCTGGGAGCTATTTGGTATCCGGCCC
GATGATTACTTGTATTCCCTCTGCAGTGAGCCGCTGATTGAACTTTGTAGCTCTGGAGCTAGCGGTTCCCTGTTCTATGC
GTCCGGCGACGATGAGTTCATTATTAAGACAGTCCGACATAAAGAGGCAGAGTTTCTGCAGAAGCTGCTTCCAGGATACT
ACATGAACCTCAACCAAAACCCTCGGACTTTGCTGCCTAAATTCTATGGACTGTACTGTGTGCAGGCAGGTGGCAAGAAC
ATTCGGATTGTGGTGATGAACAATCTTTTACCAAGGTCGGTAAAAATGCATATCAAATATGACCTCAAAGGCTCAACTAC
AAACGGCGGGCTTCCCAGAAAGAGCGAGAGAAGCCTCTTCCCACATTTAAAGACCTAGACTTCTTACAAGACATCCCTGA
TGGTCTTTTTTTGGATGCTGACGTGCACAACGCTCTCTGTAAGACCCTGCAGCGTGACTGTTTGGTGCTGCAGAGCTTCA
AGATAATGGGTTATAGCCTCTTGATGTCAATCCATAATATAGATCATGCACAACGAGAGCCCTTAAGCAGCGAAACACAA
TACTCAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCCATGGAATCCATCCAGGGAGAGGCTCG
AAGGGGTGGCACCATGGAGACCGATGACCATATGGGTGGCATCCCTGCCCGGAATAGTAAAGGGGAAAGGCTTCTGCTTT
ATATTGGCATCATTGACATTCTACAGTCTTACAGGTTTGTTAAGAAGTTGGAGCACTCTTGGAAAGCCCTGGTACATGAT
GGAGATACTGTCTCAGTGCATCACCCAGGCTTCTACGCTGAACGGTTCCAGCGCTTCATCTGCAACACAGTATTTAAGAA
GATTCCCTTGAAGCCTTCTCCTTCCAAAAGATTTCGGTCTGGCTCATCTTTCTCTCAGCGAGCAGGCTCCAGTGGCAACT
CCTGCATTACTTACCAGCCATTGGTCTCTGGGGAACACAAGGCACAAGTGACAACAAAGGCGGAAGTGGAGCCAGGCGTT
TACCTTGGTCGTCCTGATGTTTTACCTCAGACTCCACCTTTGGAGGAAATCAGTGAGGGCTCACCTATTCCTGATCCCAG
TTTCTCACCTCTAGTTGGAGAGACTTTGCAAATGCTAACTACAAGT

Alignment

ORF - retro_pabe_619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.96 %
• Parental protein coverage: 85.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTTSSALKGAIQLGITHTVGSLSTKPERDVLMQDFYVVESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFR
          .TTSSALKGAIQLGITHTVGSLST.PE.DVLMQDF..VESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFR
Retrocopy ETTSSALKGAIQLGITHTVGSLSTRPESDVLMQDFHMVESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFR

Parental  YFRELFGIRPDDYLYSLCSEPLIELCSSGASGSLFYVSSDDEFIIKTVQHKEAEFLQKLLPGYYMNLNQN
          YF.ELFGIRPDDYLYSLCSEPLIELCSSGASGSLFY.S.DDEFIIKTV.HKEAEFLQKLLPGYYMNLNQN
Retrocopy YFWELFGIRPDDYLYSLCSEPLIELCSSGASGSLFYASGDDEFIIKTVRHKEAEFLQKLLPGYYMNLNQN

Parental  PRTLLPKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDLKGST-YKRRASQKEREKPLPTFKDLDFL
          PRTLLPKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDLKGST.YKRRASQKEREKPLPTFKDLDFL
Retrocopy PRTLLPKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDLKGST<YKRRASQKEREKPLPTFKDLDFL

Parental  QDIPDGLFLDADMYNALCKTLQRDCLVLQSFKIMDYSLLMSIHNIDHAQREPLSSETQYSVDTRRPAPQK
          QDIPDGLFLDAD..NALCKTLQRDCLVLQSFKIM.YSLLMSIHNIDHAQREPLSSETQYSVDTRRPAPQK
Retrocopy QDIPDGLFLDADVHNALCKTLQRDCLVLQSFKIMGYSLLMSIHNIDHAQREPLSSETQYSVDTRRPAPQK

Parental  ALYSTAMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDGD
          ALYSTAMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDGD
Retrocopy ALYSTAMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDGD

Parental  TVSVHRPGFYAERFQRFMCNTVFKKIPLKPSPSKKFRSGSSFSRRAGSSGNSCITYQPSVSGEHKAQVTT
          TVSVH.PGFYAERFQRF.CNTVFKKIPLKPSPSK.FRSGSSFS.RAGSSGNSCITYQP.VSGEHKAQVTT
Retrocopy TVSVHHPGFYAERFQRFICNTVFKKIPLKPSPSKRFRSGSSFSQRAGSSGNSCITYQPLVSGEHKAQVTT

Parental  KAEVEPGVHLGRPDVLPQTPPLEEISEGSPIPDPSFSPLVGETLQMLTTS
          KAEVEPGV.LGRPDVLPQTPPLEEISEGSPIPDPSFSPLVGETLQMLTTS
Retrocopy KAEVEPGVYLGRPDVLPQTPPLEEISEGSPIPDPSFSPLVGETLQMLTTS

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	0.12 RPM	28.33 RPM
SRP007412_heart	0.00 RPM	17.16 RPM
SRP007412_kidney	0.00 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_619 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_619 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_619 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_716
Pan troglodytes	retro_ptro_511
Gorilla gorilla	retro_ggor_606

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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,