RetrogeneDB ID: retro_hsap_2032

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:16021392..16022634(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000267056
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSG00000151151
• Aliases: None
• Description: inositol polyphosphate multikinase [Source:HGNC Symbol;Acc:20739]

Sequence

>retro_hsap_2032
ATGGCAAGAGAGCCACCATCCCCGCTCCGGGTCGAGGCGCCGGGTCCCCCAGAAATGCGGACCCCACCGGCGATCGAGGC
CACCCCTAAGGGCACCCTGCAGCCGGCAGGCGGCAGACTCCGCTTCCTCAGTGGCTGTGTGCCCATCTTGCATCAGGTGG
CCGGGCACAGGTATGGGAAGGACAAAATGGGTATACTGCAACATCCAGATGGCACAGTTTTGAAACAGTTACAACCACCT
CCAAGGGGCCCAAGAGAGCTGGAATTCTATAATATGGTTTATGCTGCTGACTGTACCGATGGTGTTCTTCTAGAGCTACG
ACAATATTTGCCAAAATATTATGGCATCTGGCCACCTCCCGCTGCCCCAAACGATTTATACCTAAAACTGGAAAATGTGA
CCCATAAATTTAATAAGCCCTGTATAATGGATGTAAAGACAGGGCAAAAAAGCTATGATCCTTTTTGCCTCATCTGAGAA
AATTCAGCAATAGGTCAGCAAGGACCCATTAATGGAAGAGATTGGGTTCTTGGTGCTTGGCATGAGGGTTTATCTTGTTC
ATTCCCATAGCTATGAGACACAAACCAACATTATGGAAGAAGCTTAACAAAAGAAGCTATAAAGGATGGAGTCTTCGGAT
TTTTTCATAATGGGTACTGCTTAATAAAAGATGCTGTTGCTGCCATTATTCAGAAGACTGAGAAAATTCTGCAGTGGTTT
GAAAACCAGAAGCAGCTTAACTTTTACGCAAGTTCATTACTGTTTCTTTAGGAAGGTTCATCTCAGCCAATCACTACAAA
ACTGAATGACAGAAATTTGGCAGAAAAGTTTTTGTCCAAAGGACAACTGTCAGACACAGAAGTACTAGAGTGCAATAATA
ACTTTCATGTATTAACTTCCACAGTGAATGGAAAAATAGAGGCTTCAGTAGGCAAAAGCTTGTCCAAGATGTATGCCCAT
CACAGGAAAATGTATACAAAAAAGTATCACAGTCAGACTTCATTGAAAGTTGAAAATCTAGAGCAAGACAATGGGTGGAA
AAGCATGTCACAGGAACATTTAAATGGAAATGTACTTTCCCAACTGGAAAAAGTTGTCTACCATCTTCCCACTGGTTGCC
AAGAGACTGCTGAAGTGTGCATGATAGATATGGCTGATATGTTCCTTAGCAACACAGTAGATAAGGGATATGTTTATGGG
CTAAAGCATTTAATTTCTGTACTTCGAAGTATTTTAGACAAT

Alignment

ORF - retro_hsap_2032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATEPPSPLRVEAPGPPEMRTSPAIESTPEGTPQPAGGRLRFLNGCVPLSHQVAGHMYGKDKVGILQHPD
          MA.EPPSPLRVEAPGPPEMRT.PAIE.TP.GT.QPAGGRLRFL.GCVP..HQVAGH.YGKDK.GILQHPD
Retrocopy MAREPPSPLRVEAPGPPEMRTPPAIEATPKGTLQPAGGRLRFLSGCVPILHQVAGHRYGKDKMGILQHPD

Parental  GTVLKQLQPPPRGPRELEFYNMVYAADCFDGVLLELRKYLPKYYGIWSPPTAPNDLYLKLEDVTHKFNKP
          GTVLKQLQPPPRGPRELEFYNMVYAADC.DGVLLELR.YLPKYYGIW.PP.APNDLYLKLE.VTHKFNKP
Retrocopy GTVLKQLQPPPRGPRELEFYNMVYAADCTDGVLLELRQYLPKYYGIWPPPAAPNDLYLKLENVTHKFNKP

Parental  CIMDVKIGQKSYDPF-ASSEKIQQQVSKYPLMEEIGFLVLGMRVYHVHSDSYETE-NQHYGRSLTKETIK
          CIMDVK.GQKSYDPF.ASSEKIQQ.VSK.PLMEEIGFLVLGMRVY.VHS.SYET..NQHYGRSLTKE.IK
Retrocopy CIMDVKTGQKSYDPF>ASSEKIQQ*VSKDPLMEEIGFLVLGMRVYLVHSHSYETQ<NQHYGRSLTKEAIK

Parental  DGVSRFFHNGYCLRKDAVAASIQKIEKILQWFENQKQLNFYASSLLFVYEGSSQPTTTKLNDRTLAEKFL
          DGV..FFHNGYCL.KDAVAA.IQK.EKILQWFENQKQLNFYASSLLF..EGSSQP.TTKLNDR.LAEKFL
Retrocopy DGVFGFFHNGYCLIKDAVAAIIQKTEKILQWFENQKQLNFYASSLLFL*EGSSQPITTKLNDRNLAEKFL

Parental  SKGQLSDTEVLEYNNNFHVLSSTANGKIESSVGKSLSKMYARHRKIYTKKHHSQTSLKVENLEQDNGWKS
          SKGQLSDTEVLE.NNNFHVL.ST.NGKIE.SVGKSLSKMYA.HRK.YTKK.HSQTSLKVENLEQDNGWKS
Retrocopy SKGQLSDTEVLECNNNFHVLTSTVNGKIEASVGKSLSKMYAHHRKMYTKKYHSQTSLKVENLEQDNGWKS

Parental  MSQEHLNGNVLSQLEKVFYHLPTGCQEIAEVEVRMIDFAHVFPSNTIDEGYVYGLKHLISVLRSILDN
          MSQEHLNGNVLSQLEKV.YHLPTGCQE.A..EV.MID.A..F.SNT.D.GYVYGLKHLISVLRSILDN
Retrocopy MSQEHLNGNVLSQLEKVVYHLPTGCQETA--EVCMIDMADMFLSNTVDKGYVYGLKHLISVLRSILDN

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
bodymap2_adipose	0.16 RPM	29.22 RPM
bodymap2_adrenal	0.08 RPM	17.79 RPM
bodymap2_brain	3.12 RPM	15.54 RPM
bodymap2_breast	0.04 RPM	20.60 RPM
bodymap2_colon	0.00 RPM	25.56 RPM
bodymap2_heart	0.00 RPM	7.92 RPM
bodymap2_kidney	2.17 RPM	17.48 RPM
bodymap2_liver	9.51 RPM	9.97 RPM
bodymap2_lung	0.35 RPM	35.64 RPM
bodymap2_lymph_node	0.16 RPM	28.49 RPM
bodymap2_ovary	0.29 RPM	8.85 RPM
bodymap2_prostate	0.74 RPM	14.58 RPM
bodymap2_skeletal_muscle	0.00 RPM	11.59 RPM
bodymap2_testis	0.09 RPM	15.50 RPM
bodymap2_thyroid	0.13 RPM	13.37 RPM
bodymap2_white_blood_cells	0.00 RPM	96.65 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2032 was not detected

EST

2 EST(s) were mapped to retro_hsap_2032 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI199420	16021664	16022085	99.8	420	1	419
CB050949	16021500	16021762	99.7	261	1	260

TSS

No TSS is located nearby retro_hsap_2032 retrocopy 5' end.

Lab

retro_hsap_2032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2032 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,