RetrogeneDB ID: retro_ptro_2389

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:122856957..122858090(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSPTRG00000010813
• Aliases: None
• Description: None

Sequence

>retro_ptro_2389
TGTGAGCCACCAAAACCACAGTGTTCTTTGCCTGAAGACCCAGCTATCCTTCAGTCCTCACTAGGCTCATCAACTTCTTC
ATTCTGGTGCGTGGGGTTCTCATGGGCCTTTGGGCAGGATGCTCATATACAGTCGGTTCAGTCCAACCTCCTTAGTTGGG
CAGGAGTTTGGTGCCGTTGCTGTTGCTGGAAGCTCTTTGATATCGTTTGGAACAGAAACATCAAACAGTGGTGTCTTACC
CCAAAGTAGTATGGTTGACTCTGCCTTAACACAGGATACAAGATCTCTAAAAACACAGTTATCTCAAGGTCACTCAAGCC
CTCAGTTAGACCCTTTGAGAAAAAGCCCAACCACTGAACAAGCAGTGAAGACTGTCTCGGCCCATTTACCTGCTCCAGCA
CCTGTTGGGAGAAGGAGCCCTGTATCAACTAGGCCTTTGCCATCTACCAGCCAAAAAGCAATAGAGATCAAGAGCACTGG
TGAGCTGAAGTACACAATGTTTCAAGACCAGAAAATGAGCAACTCAGAAATGATAGCAAGAGACAAGTAGCTCCAGGTAC
TCCTTCAGCTCCAAGGAGAGGGCGTGGGGTTCAGCCGGGTAGCAGGGGAAGATTTGGTATTCTGCGAGATGGGCCAATGA
AATTTGAGAAAGACTTTGACTTTGAAAGTGCAAATGCACAATTCAACAAAGGAGAGATCGACAGAGAGTTTCATAATAAA
CTTAAAAGAAGATAAACTGAGAAACAGGAGGAGCCTGTAAATAGTGAAGATAAAGGTGACCCAGGAGTTGATACCCCAAA
AGTAAAGGAAATGCTGATGAAGAAGATCCACTTGGACCTAACTGCTAGTAGGAAAAAACTAAATCCTTCTTTGATAATAT
TTCTTGTGATGACAATAGGGAACGGATATCAACCTGGGCTGAAGAAAGAAGATTAAATGCTGAAGCATTTGGAATCCCAC
TTTGTCCAAATCGTGGCTGTGGGAGACGCAGAGGCAGAGGGATCTTTGGTTTCTGTGGTGGCAGAGGGCATGGTGGTAGC
AGATGTGGTACTTTAACCATCCCTGGAGGATTTCGCAGTGGATTCAGAGGAGGTCCTGGGGGCAGGGAGTTTTCGGATTT
CTAATGTAGGAAA

Alignment

ORF - retro_ptro_2389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.16 %
• Parental protein coverage: 82.07 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CEPPKPQCSLPQDPAIVQSSLGSSTSSFQSMG-SYGPFGRMPTYSQFSPSSLVGQQFGAVGVAGSSLTSF
          CEPPKPQCSLP.DPAI.QSSLGSSTSSF...G.S.GP.GRM..YS.FSP.SLVGQ.FGAV.VAGSSL.SF
Retrocopy CEPPKPQCSLPEDPAILQSSLGSSTSSFWCVG>SHGPLGRMLIYSRFSPTSLVGQEFGAVAVAGSSLISF

Parental  GTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQTASAHVPAPAAVGRRS
          GTETSNSG.LPQSS.V.SA.TQDTRSLKTQLSQG.SSPQLDPLRKSPT.EQAV.T.SAH.PAPA.VGRRS
Retrocopy GTETSNSGVLPQSSMVDSALTQDTRSLKTQLSQGHSSPQLDPLRKSPTTEQAVKTVSAHLPAPAPVGRRS

Parental  PVSTRPLPSASQKAGE-NQEHRRAEVHKVSRPENEQLRNDSKRQVAPGAPSAPRRGRGGHRGGRGRFGIR
          PVSTRPLPS.SQKA.E..QEH..AEVH.VSRPENEQLRNDSKRQVAPG.PSAPRRGRG...G.RGRFGI.
Retrocopy PVSTRPLPSTSQKAIE<DQEHW*AEVHNVSRPENEQLRNDSKRQVAPGTPSAPRRGRGVQPGSRGRFGIL

Parental  RDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDT-QNSEGNADEE
          RDGPMKFEKDFDFESANAQFNK.EIDREFHNKLK......EKQE.PVN.EDKGD.GVDT...S.GNADEE
Retrocopy RDGPMKFEKDFDFESANAQFNKGEIDREFHNKLKRR--*TEKQEEPVNSEDKGDPGVDT<PKSKGNADEE

Parental  DPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGGLGFRGGRGRG
          DPLGPNC...KTKSFFDNISCDDNRER..TWAEERRLNAE.FGIPL.PNRG.G..RGRG..GF.GGRG.G
Retrocopy DPLGPNC**EKTKSFFDNISCDDNRERISTWAEERRLNAEAFGIPLCPNRGCGRRRGRGIFGFCGGRGHG

Parental  GGRGGTFTAPRGFRGGFRGGRGGREFADFEYRK
          G.R.GT.T.P.GFR.GFRGG.GGREF.DF..RK
Retrocopy GSRCGTLTIPGGFRSGFRGGPGGREFSDF*CRK

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	35.53 RPM
SRP007412_cerebellum	0.04 RPM	54.17 RPM
SRP007412_heart	0.00 RPM	41.53 RPM
SRP007412_kidney	0.03 RPM	58.79 RPM
SRP007412_liver	0.00 RPM	37.06 RPM
SRP007412_testis	0.00 RPM	139.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2389 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2389 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2378
Pongo abelii	retro_pabe_2906
Macaca mulatta	retro_mmul_1860

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389 , retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,