RetrogeneDB ID: retro_ptro_1351

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:16175667..16176909(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSPTRG00000002516
• Aliases: None
• Description: None

Sequence

>retro_ptro_1351
ATGGCAAGAGAGCCACCATCCCCGCTCCGGGTCGAGGCGCCGGGTCCCCCAGAAATGCGGACCCCACCGGCGATCGAGGC
CACCCCTAAGGGCACCCTGCAGCCGGCAGGCGGCAGACTCCGCTTCCTCAGTGGCTGTGTGCCCATCTTGCATCAGGTGG
CCGGGCACAGGTATGGGAAGGACAAAATGTGTATACTGCAACATCCAGATGGCACAGTTTTGAAACAGTTACAACCACCT
CCAAGGGGCCCAAGAGAGCTGGAATTCTATAATATGGTTTATGCTGCTGACTGTACCGATGGTGTTCTTCTAGAGCTACG
ACAATATTTGCCAAAATATTATGGCATCTGGCCACCTCCCGCTGCCCCAAACGATTTATACCTAAAACTGGAAAATGTGA
CCCATAATTTTAATAAGCCCTGTATAATGGATGTAAAGACAGGGCAAAAAAGCTATGATCCTTTTTGCCTCATCTGAGAA
AATTCAGCAACAGGTCAGCAAGGACCCATTAATGGAAGAGATTGGGTTCTTGGTGCTTGGCATGAGGGTTTATCTTGTTC
ATTCCCATAGCTATGAGACACAAACCAACATTATGGAAGAAGCTTAACAAAAGAAGCTATAAAGGATGGAGTCTCCGGAT
TTTTTCATAATGGGTACTGCTTAATAAAAGATGCTGTTGCTGCCATTATTCAGAAGACTGAGAAAATTCTGCAGTGGTTT
GAAAACCAGAAGCAGCTTAACTTTTACGCAAGTTCATTACTGTTTCTTTAGGAAGGTTCATCTCAGCCAATCACTACAAA
ACTGAATGACAGAAATTTGGCAGAAAAGTTTTTGTCCAAAGGACAACTGTCAGACACAGAAGTACTAGAGTGCAATAATA
ACTTTCATGTATTAACTTCCACAGTGAATGGAAAAATAGAGGCTTCAGTAGGCAAAAGCTTGTCCAAGATGTATGCCCAT
CACAGGAAAATGTATACAAAAAAGTATCACAGTCAGACTTCATTGAAAGTTGAAAATCTGGAGCAAGACAATGGGTGGAA
AAGCATGTCACAGGAACATTTAAATGGGAATGTACTTTCCCAACTGGAAAAAGTTGTCTACCATCTTCCCACTGGTTGCC
AAGAGACTGCTGAAGTGCGCATGATAGATATGGCTGATATGTTCCTTAGCAACACAGTAGATAAGGGATATGTTTATGGG
CTAAAGCATTTAATTTCTGTACTTCGAAGTATTTTAGACAAT

Alignment

ORF - retro_ptro_1351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATEPPSPLRVEAPGPPEMRTSPAIESTPEGTPQPAGGRLRFLNGCVPLSHQVAGHMYGKDKVGILQHPD
          MA.EPPSPLRVEAPGPPEMRT.PAIE.TP.GT.QPAGGRLRFL.GCVP..HQVAGH.YGKDK..ILQHPD
Retrocopy MAREPPSPLRVEAPGPPEMRTPPAIEATPKGTLQPAGGRLRFLSGCVPILHQVAGHRYGKDKMCILQHPD

Parental  GTVLKQLQPPPRGPRELEFYNMVYAADCFDGVLLELRKYLPKYYGIWSPPTAPNDLYLKLEDVTHKFNKP
          GTVLKQLQPPPRGPRELEFYNMVYAADC.DGVLLELR.YLPKYYGIW.PP.APNDLYLKLE.VTH.FNKP
Retrocopy GTVLKQLQPPPRGPRELEFYNMVYAADCTDGVLLELRQYLPKYYGIWPPPAAPNDLYLKLENVTHNFNKP

Parental  CIMDVKIGQKSYDPF-ASSEKIQQQVSKYPLMEEIGFLVLGMRVYHVHSDSYETQ-NQHYGRSLTKETIK
          CIMDVK.GQKSYDPF.ASSEKIQQQVSK.PLMEEIGFLVLGMRVY.VHS.SYETQ.NQHYGRSLTKE.IK
Retrocopy CIMDVKTGQKSYDPF>ASSEKIQQQVSKDPLMEEIGFLVLGMRVYLVHSHSYETQ<NQHYGRSLTKEAIK

Parental  DGVSRFFHNGYCLRKDAVAASIQKIEKILQWFENQKQLNFYASSLLFVYEGSSQPTTTKLNDRTLAEKFL
          DGVS.FFHNGYCL.KDAVAA.IQK.EKILQWFENQKQLNFYASSLLF..EGSSQP.TTKLNDR.LAEKFL
Retrocopy DGVSGFFHNGYCLIKDAVAAIIQKTEKILQWFENQKQLNFYASSLLFL*EGSSQPITTKLNDRNLAEKFL

Parental  SKGQLSDTEVLEYNNNFHVLSSTANGKIESSVGKSLSKIYARHRKIYTKKHHSQTSLKVENLEQDNGWKS
          SKGQLSDTEVLE.NNNFHVL.ST.NGKIE.SVGKSLSK.YA.HRK.YTKK.HSQTSLKVENLEQDNGWKS
Retrocopy SKGQLSDTEVLECNNNFHVLTSTVNGKIEASVGKSLSKMYAHHRKMYTKKYHSQTSLKVENLEQDNGWKS

Parental  MSQEHLNGNVLSQLEKVFYHLPTGCQEIAEVEVRMIDFAHVFPSNTIDEGYVYGLKHLISVLRSILDN
          MSQEHLNGNVLSQLEKV.YHLPTGCQE.A..EVRMID.A..F.SNT.D.GYVYGLKHLISVLRSILDN
Retrocopy MSQEHLNGNVLSQLEKVVYHLPTGCQETA--EVRMIDMADMFLSNTVDKGYVYGLKHLISVLRSILDN

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	5.70 RPM
SRP007412_cerebellum	0.00 RPM	5.81 RPM
SRP007412_heart	0.00 RPM	2.86 RPM
SRP007412_kidney	0.00 RPM	5.73 RPM
SRP007412_liver	0.10 RPM	4.06 RPM
SRP007412_testis	0.00 RPM	5.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1351 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1351 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1351 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,