RetrogeneDB ID: retro_pabe_1035

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:21989863..21991095(-)
• 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_1035
ATGGCAAAAGAGCCACCATCACCCCTCCGGGTCGAGGCGCTGGCCCCCCGGAATTGTGGGCCTCACCGGCGATCGAGGCC
ATCCCTGAGGGCACCCCGCAGCCGGCGGGCGGCAGGCTCCGCTTCCTCAAAGGCTAAGTGCCCCTCTCGCATCAGGTGGC
CGGACACATGAACGGGAAGGACAAAGTGGGTATACTGCAACACCCAGATGGCACAGTTTTGAAACAGTTACAACCACCTC
CAAGGGGCCCAAGAGAGCATATGGTTTATGCTGCTGACTGTTCTGATGGTGTTCTTCTAGAGCTACGAAAATATTTGCCA
AAATGTGGCATCTGGTCACCTCCCACTGCACCAAACGATGTATACCTAAAACTGGAAGATGTGACCCATAAATTTAATAA
GCCTTGTATAATGAATATAAAGATCGGGCAAAAAAGCTATGATCCTTTTGCCTCGTCTGAGAAGATTCAGCAACAGGTCA
GCAAGTACCCATTAATGGAAGAGATTGGGTTTCTTGGTGCTTGGCATGAGGGTTTACCATGTTCATTCCGATAGCTATGA
TATACCAAACCAGCATTATGGAAGAAGCTTAACAAAAGAAACTATAAAGGATGGAGTCTCCGGATTTTTTCATAATGGGT
ACTGCTTAAGAAAAGATGCTGTTGCTGCCAGTATTCAGAAGATTGAGAAAATTCTGTAGTGGTGTGAAAACCAGAAGCAG
CTTAACTTTTATGCAAGTTCATTACTATTGGTTTATGAAAGTTCGTCTCAGCCAACCACTACAAAATTGAATGACAGAAC
TTTGGCAGAAACATTTTTGTCCAAAGGACAACTGTCAGACACAGAGGTACTAGAGTACAATAATAACTTTCATGTGTTAA
GTTCCACAGCGAATGGAAAAATAGAGGCTTAAGTGGGCAAAAGCTTGTCCAAGATGTATGCTCGTCACAGGAAAATGTAT
ACAAAAACCATCACAGTCAGACTTCAGTGAAAGTTGAAAATCTGGAGCAAGACAATGGGTGGAAAAGCATGTCACAGGAA
CATTTAAATGGAAATGCACTTTCCCAACTGGAAAAAGTTTTCTACCATCTTCCCACTGGTTGCCAAGAGATTGCTGAAGT
AGGAGTGCAAATGATAGATTTCGCTTATGTGTTCTCTAGCAGCACAATAGATGAGGGATATAGTTATGGGCTAAAGCATT
TAATTTCTGTACTTCGAAGTATTTTAGACAAT

Alignment

ORF - retro_pabe_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATEPPSPLRVEA-PGPPEMRTPPAIESTPEGTPQPAGGRLRFLNGCVPLSHQVAGHMYGKDKVGILQHP
          MA.EPPSPLRVEA..GPPE....PAIE..PEGTPQPAGGRLRFL.G.VPLSHQVAGHM.GKDKVGILQHP
Retrocopy MAKEPPSPLRVEA<AGPPELWASPAIEAIPEGTPQPAGGRLRFLKG*VPLSHQVAGHMNGKDKVGILQHP

Parental  DGTVLKQLQPPPRGPRELEFYNMVYAADCFDGVLLELRKYLPKYYGIWSPPTAPNDLYLKLEDVTHKFNK
          DGTVLKQLQPPPRGPRE.....MVYAADC.DGVLLELRKYLPK..GIWSPPTAPND.YLKLEDVTHKFNK
Retrocopy DGTVLKQLQPPPRGPRE----HMVYAADCSDGVLLELRKYLPKC-GIWSPPTAPNDVYLKLEDVTHKFNK

Parental  PCIMDVKIGQKSYDPFASSEKIQQQVSKYPLMEEIGFL-VLGMRVYHVHSDSYETQNQHYGRSLTKETIK
          PCIM..KIGQKSYDPFASSEKIQQQVSKYPLMEEIGFL.VLGMRVYHVHSDSY...NQHYGRSLTKETIK
Retrocopy PCIMNIKIGQKSYDPFASSEKIQQQVSKYPLMEEIGFL>VLGMRVYHVHSDSYDIPNQHYGRSLTKETIK

Parental  DGVSRFFHNGYCLRKDAVAASIQKIEKILQWFENQKQLNFYASSLLFVYEGSSQPTTTKLNDRTLAEKFL
          DGVS.FFHNGYCLRKDAVAASIQKIEKIL.W.ENQKQLNFYASSLL.VYE.SSQPTTTKLNDRTLAE.FL
Retrocopy DGVSGFFHNGYCLRKDAVAASIQKIEKIL*WCENQKQLNFYASSLLLVYESSSQPTTTKLNDRTLAETFL

Parental  SKGQLSDTEVLEYNNNFHVLSSTANGKIESSVGKSLSKMYARHRKMYT-KKHHSQTSLKVENLEQDNGWK
          SKGQLSDTEVLEYNNNFHVLSSTANGKIE..VGKSLSKMYARHRKMYT.K.HHSQTS.KVENLEQDNGWK
Retrocopy SKGQLSDTEVLEYNNNFHVLSSTANGKIEA*VGKSLSKMYARHRKMYT<KNHHSQTSVKVENLEQDNGWK

Parental  SMSQEHLNGNVLSQLEKVFYHLPTGCQEVAEVEVRMIDFAHVFPSNTIDEGYVYGLKHLISVLRSILDN
          SMSQEHLNGN.LSQLEKVFYHLPTGCQE.AEV.V.MIDFA.VF.S.TIDEGY.YGLKHLISVLRSILDN
Retrocopy SMSQEHLNGNALSQLEKVFYHLPTGCQEIAEVGVQMIDFAYVFSSSTIDEGYSYGLKHLISVLRSILDN

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	0.06 RPM	1.11 RPM
SRP007412_cerebellum	0.24 RPM	2.68 RPM
SRP007412_heart	0.00 RPM	0.78 RPM
SRP007412_kidney	0.00 RPM	0.70 RPM
SRP007412_liver	0.00 RPM	1.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1035 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1035 has 0 orthologous retrocopies within eutheria group .

---

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,