RetrogeneDB ID: retro_ptro_1343

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:59135821..59137185(+)
• 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_1343
CCTTTGACATCAGCAAGCATCAGCCTCCTGTCCGAGGCGGAGATCCGCCACGAGGGCATCCTCTGCACCGTCGACACCGA
ACACTTCACCGCAGCCCTCGCCAAAGTTCGATCCTTTGGTCCAGAAGGCAGACCGACAGATGGTCCAATACCGCCTCGAG
ATGGAGTCTTTGAATACATTAAATTCCGTGGGAGTGACGTGAAAGACCTCACTGTCTGCGAGCCACCAAAACCACGGTGT
TCTTTGCCTCAAGACCCAGCTATCGTTCAGTTCTCACCAGGCTCATCGACTTCTTCATTCCAGTCCATGGGTTCTTCTGG
GCCTTTCGGCAGGATGGCCACATCCAGCCAGTTCAGTCCAGGTTCCTTAGTGGGGCAGCAGTTTGGTGCTGTTGCTGTTG
CTGGAAGCTCTTTGACCTCCTTTGGAACAGAAATATCAAACAGTGGTACCTTGCCCCAACGTAGTGCGGTTGGTTCTGCC
TTTACACAGGATACAAGAATCTCTAAAAACACAATTATCTCAGGGTCGTTCAAGCGCGCAGTTCGACCCTTTGAGGAGAA
GCCCAACCATGGAACAAGGAGTGCAGACCCCCGGGCCCACTTACCTGCTCCAGCACCTGTTGGTAGAAGGAGTCCTGTAT
CAACCAGGCCTTTGCCATCTACCAGCCAAAAAGCAATAGAGAATCAGGAGCAGAGGTGAGCTGAAGCGCACAACGTTCCA
AGGCCAGAAAATGAGCAACTCAGAAATGCAACAAGAGACAAGCAGCTCCAGGTGCTCCTTCAGCGCCAAGGAGAGGGCGT
GGGAGTCTTCGGCGTGGCAGGGGAAGATTTGGTATTCGGCGAGATGGGCCAATGAAATTTGAGAAAGACTTTGAAAGTGC
AAATGCACAATTCAACAAGGAAGAGATGGGCAGAGAGTTTCATAATAAACTTAAATTAAAAGAAGATAAACTTGAGAAAC
AGGAGAAGCTTATAAATAGTGAAGATAAAGGAGACTCAGGAGTTGATACTCAAAGCAGTGAAGGACATGCTGATGAAGAT
GCACTTGGACCTAATTGCTATTATGACCAAACTAAATCCTCCTTTGATAATATTTCTGGTGATGACAATAGAGAACGGAG
GCCAACCTGGGCTGAAGGAAGAAGATTAAATGCTGAAACATTTGGAATCCCACTTTGTCCAAACCGTGGCCGTGGGGGAT
ACAGAGGCAGAGGAGGTCTTGGTTTCCGTGGTGGCAGAGGGCGTGGTGGTGGCAGAGGTGGTACCTTGACCACCCCTTGA
GGATTTCGAGGTGGATTCAGAGGAGGTTCCAGGGGTCGGGAGTTTGCAGATTTTGAATATAGGAAAAGCACGGCCTTTGG
CCCC

Alignment

ORF - retro_ptro_1343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.73 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSDIKDL
          P.....ISL.S.AEIR.EGIL.T.DTE..T.ALAKVRSFG.E.RPTD.PIPPRD.VFEYI.FRGSD.KDL
Retrocopy PLTSASISLLSEAEIRHEGILCTVDTEHFTAALAKVRSFGPEGRPTDGPIPPRDGVFEYIKFRGSDVKDL

Parental  TVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQSMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVAGSSLTS
          TVCEPPKP.CSLPQDPAIVQ.S.GSSTSSFQSMGS.GPFGRM.T.SQFSP.SLVGQQFGAV.VAGSSLTS
Retrocopy TVCEPPKPRCSLPQDPAIVQFSPGSSTSSFQSMGSSGPFGRMATSSQFSPGSLVGQQFGAVAVAGSSLTS

Parental  FGTETSNSGTLPQSSAVGSAFTQDTR-SLKTQLSQGRSSPQLDPLRKSPTMEQAVQTAS-AHVPAPAAVG
          FGTE.SNSGTLPQ.SAVGSAFTQDTR.SLKTQLSQGRSS.Q.DPLR.SPTMEQ.VQT...AH.PAPA.VG
Retrocopy FGTEISNSGTLPQRSAVGSAFTQDTR>SLKTQLSQGRSSAQFDPLRRSPTMEQGVQTPG<AHLPAPAPVG

Parental  RRSPVSTRPLPSASQKAGENQEHRRAEVHKVSRPENEQLRND-SKRQVAPGAPSAPRRGRGGHRGGRGRF
          RRSPVSTRPLPS.SQKA.ENQE.R.AE.H.V.RPENEQLRN...KRQ.APGAPSAPRRGRG..R.GRGRF
Retrocopy RRSPVSTRPLPSTSQKAIENQEQR*AEAHNVPRPENEQLRNA<NKRQAAPGAPSAPRRGRGSLRRGRGRF

Parental  GIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDTQNSEGNAD
          GIRRDGPMKFEK..DFESANAQFNKEE..REFHNKLKLKEDKLEKQEK..N.EDKGDSGVDTQ.SEG.AD
Retrocopy GIRRDGPMKFEK--DFESANAQFNKEEMGREFHNKLKLKEDKLEKQEKLINSEDKGDSGVDTQSSEGHAD

Parental  EEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGGLGFRGGRG
          .ED.LGPNCYYD.TKS.FDNIS.DDNRERRPTWAE.RRLNAETFGIPL.PNRGRGGYRGRGGLGFRGGRG
Retrocopy -EDALGPNCYYDQTKSSFDNISGDDNRERRPTWAEGRRLNAETFGIPLCPNRGRGGYRGRGGLGFRGGRG

Parental  RGGGRGGTFTAPRGFRGGFRGGRGGREFADFEYRKTTAFGP
          RGGGRGGT.T.P.GFRGGFRGG..GREFADFEYRK.TAFGP
Retrocopy RGGGRGGTLTTP*GFRGGFRGGSRGREFADFEYRKSTAFGP

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	0.29 RPM	35.53 RPM
SRP007412_cerebellum	0.22 RPM	54.17 RPM
SRP007412_heart	0.12 RPM	41.53 RPM
SRP007412_kidney	0.21 RPM	58.79 RPM
SRP007412_liver	0.20 RPM	37.06 RPM
SRP007412_testis	0.53 RPM	139.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1343 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1343 has 0 orthologous retrocopies within eutheria group .

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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,