RetrogeneDB ID: retro_pabe_1689

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19_random:287743..288378(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSPPYG00000002433
• Aliases: None
• Description: inositol polyphosphate multikinase [Source:HGNC Symbol;Acc:20739]

Sequence

>retro_pabe_1689
ATGGCAAGAGAGCCACCATCCCCGCTCCGGGTCGAGGCGCCGGGTCCCCCAGAAATGCGGACCCCACCGGCGATCGAGGC
CACCCCTGAGGGCACCCCGCAGCCGGCAGGCGGCAGACTCCGTTTCCTCAACGGCTGCGTGCCCATCTCGCATCAGGTGG
CCAGGCACAGGTATGGGAAGGACAAAATGGGTATACTGCAACATCCAGATGGCAGTTTTGAAACAGTTACAACCACCTCC
AAGGGGCCCCAAGACAGCTGGAATTCTATAATATGGTCTATGCTGATGACTGTACCGATGGTGTTCTTCTAGAGCCACGA
CAATATTTGCCAAAATATTATGACATCTGGCCACCTCCCACTGCCCCAAACGATTTATACCTAAAACTGGAAGATGTGAC
CCATAAATTTAATAAGCCCTGTATAGTGGATGTAAAGACAGGGCAAAAAAGCTATGATCCTTTTTGCCTCATCTGAGAAG
ATTCAGCAACAGGTCAGCAAGGACCCATTAATGGAAGAGATTGGGTTCTTGGTGCTTGGCATGAGGGTTTATCTTGTTCA
TTCCCATAGCTATGAGACACAAACCAACATTACGGAAGAAGCTTAACAAAAGAAACTATAAAGGATGGAGTCTCT

Alignment

ORF - retro_pabe_1689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.11 %
• Parental protein coverage: 50.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MATEPPSPLRVEAPGPPEMRTPPAIESTPEGTPQPAGGRLRFLNGCVPLSHQVAGHMYGKDKVGILQHPD
          MA.EPPSPLRVEAPGPPEMRTPPAIE.TPEGTPQPAGGRLRFLNGCVP.SHQVA.H.YGKDK.GILQHPD
Retrocopy MAREPPSPLRVEAPGPPEMRTPPAIEATPEGTPQPAGGRLRFLNGCVPISHQVARHRYGKDKMGILQHPD

Parental  GT-VLKQLQPPPRGP-RELEFYNMVYAADCFDGVLLELRKYLPKYYGIWSPPTAPNDLYLKLEDVTHKFN
          G........PP.RGP.R.LEFYNMVYA.DC.DGVLLE.R.YLPKYY.IW.PPTAPNDLYLKLEDVTHKFN
Retrocopy GS>LKQLQPPP-RGP>RQLEFYNMVYADDCTDGVLLEPRQYLPKYYDIWPPPTAPNDLYLKLEDVTHKFN

Parental  KPCIMDVKIGQKSYDP-FASSEKIQQQVSKYPLMEEIGFLVLGMRVYHVHSDSYETQ-NQHYGRSLTKET
          KPCI.DVK.GQKSYDP.FASSEKIQQQVSK.PLMEEIGFLVLGMRVY.VHS.SYETQ.NQHYGRSLTKET
Retrocopy KPCIVDVKTGQKSYDP>FASSEKIQQQVSKDPLMEEIGFLVLGMRVYLVHSHSYETQ<NQHYGRSLTKET

Parental  IKDGVS
          IKDGVS
Retrocopy IKDGVS

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	1.11 RPM
SRP007412_cerebellum	0.00 RPM	2.68 RPM
SRP007412_heart	0.00 RPM	0.78 RPM
SRP007412_kidney	0.00 RPM	0.70 RPM
SRP007412_liver	0.06 RPM	1.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1689 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1689 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000011011	1 retrocopy	retro_apla_14,
Cavia porcellus	ENSCPOG00000000222	1 retrocopy	retro_cpor_369,
Erinaceus europaeus	ENSEEUG00000009958	1 retrocopy	retro_eeur_110,
Homo sapiens	ENSG00000151151	2 retrocopies	retro_hsap_1244, retro_hsap_2032,
Gorilla gorilla	ENSGGOG00000008790	1 retrocopy	retro_ggor_1464,
Myotis lucifugus	ENSMLUG00000015030	1 retrocopy	retro_mluc_518,
Nomascus leucogenys	ENSNLEG00000012319	2 retrocopies	retro_nleu_2419, retro_nleu_2622,
Pongo abelii	ENSPPYG00000002433	3 retrocopies	retro_pabe_1035, retro_pabe_1086, retro_pabe_1689 ,
Pan troglodytes	ENSPTRG00000002516	2 retrocopies	retro_ptro_1351, retro_ptro_855,