RetrogeneDB ID: retro_ptro_1387

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:6084042..6085266(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNCRIP
• Ensembl ID: ENSPTRG00000018393
• Aliases: None
• Description: Synaptotagmin binding, cytoplasmic RNA interacting protein [Source:UniProtKB/TrEMBL;Acc:K7BNP6]

Sequence

>retro_ptro_1387
ATGGCTACAGAACATGTTAATGGAAATGATACTGAAGAGCTCATGGATACTACTTTTGCAGTTATCCATTCAGAAAATTT
TCAGACATTGCTTGATGCTGGTTTATCACAGAAAGTTGCTGAAAAACTAGATGAAATTTACGTTGCAGGGCTAGTTGCAC
ATAGTCATTTAGATGAAAGAGCTATTGAAGCTTTAAAAGAATTCAATGAAGACGGTGCATTGGCAGTTCTTCAACAGTTA
AAGACAGTGATCTCTCTCGTGTTCAGAACAAAAGTGCCTTTTTATGTGGAGTCATGAAACCTTACAGGCAGAGAGAAAAA
CAAGGGACCAAAGTAGCAGATTCTAGTAAAGGACCAGATGAGGCAAAAATTAAGGCACTCTTGGAAAGAGCAGGCTACAC
ACTTGATGTGACCACTGGACCGAGGAAATATGGAGGACCACCTCCAGATTCCGTTTATTCAGGTCAGCAGCCTTCTGTTG
GCACTGAGATATTTGTGGGAAAGATCCCAAGAGATCTATTTGAGGATGAACTTGTTCCATTATTTGAGAAAGCTGGTCCT
ATATGGGATCTTCGTCTAATGATGGATCCACTCACTGGTCTCAATAGAGGTTATGTGTTTGTCACTTTTTGTACAAAAGA
AGCAGCTCGGGAGGCTGTTAAAACTGTATAATAATCATGAAATTCGTTCTGGAAAACACAATGGTGTCTGCATCTCAGTT
GCCAACAATAGGCTTTTTGTGGGCTCTATTCCTAAGAGTTAAAACCAAGGAACAGATTCTTGAAGAATTTAGCAAAAGTA
ACAGAGGGTCTTACAGACGTCATTTTATACCACCAACCGGATGAGAAGAAAAAAAACAGACTTTTGCTTTCTTAAATATG
AAGATCACAAAACAGCTGCCCAGGCAAGGCGTAGGTTAATGAGTGGTAAAGTCAAGGTCTGGGGGAATGTTGGAACTGTT
GAATGGGCTGATCCTATGGAAGATCCTGATCCTGAGGTTATGGCAAAGGTAAAAGTGCTGTTTGTACGCAACCTTGCCAA
TACTGTAACGGAAGAGATTTTAGAAAAGGCATTTAGTCAGTTTGGGAAACTGGAATGAGTGAAGAAGTTAAAAGATTATC
CATTCATTCATTTTGATGAGTGAGATGGTGCTGTCAAGGCTATGGAAGAAATGAATGGTAAAGACTTGGAGGGAGAAAAT
ATTGAAATTGTTTTTGCCAAGCCA

Alignment

ORF - retro_ptro_1387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.75 %
• Parental protein coverage: 65.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MATEHVNGNGTEEPMDTTSAVIHSENFQTLLDAGLPQKVAEKLDEIYVAGLVAHSDLDERAIEALKEFNE
          MATEHVNGN.TEE.MDTT.AVIHSENFQTLLDAGL.QKVAEKLDEIYVAGLVAHS.LDERAIEALKEFNE
Retrocopy MATEHVNGNDTEELMDTTFAVIHSENFQTLLDAGLSQKVAEKLDEIYVAGLVAHSHLDERAIEALKEFNE

Parental  DGALAVLQQFK-DSDLSHVQNKSAFLCGVMKTYRQREKQGTKVADSSKGPDEAKIKALLERTGYTLDVTT
          DGALAVLQQ.K.DSDLS.VQNKSAFLCGVMK.YRQREKQGTKVADSSKGPDEAKIKALLER.GYTLDVTT
Retrocopy DGALAVLQQLK<DSDLSRVQNKSAFLCGVMKPYRQREKQGTKVADSSKGPDEAKIKALLERAGYTLDVTT

Parental  GQRKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVT
          G.RKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGY.FVT
Retrocopy GPRKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYVFVT

Parental  FCTKEAAQEAV-KLYNNHEIRSGKHIGVCISVANNRLFVGSIPKS-KTKEQILEEFS-KVTEGLTDVILY
          FCTKEAA.EAV.KLYNNHEIRSGKH.GVCISVANNRLFVGSIPKS.KTKEQILEEFS.KVTEGLTDVILY
Retrocopy FCTKEAAREAV>KLYNNHEIRSGKHNGVCISVANNRLFVGSIPKS>KTKEQILEEFS>KVTEGLTDVILY

Parental  HQPDDKKKNR-GFCF-LEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIEDPDPEVMAKVKVLFVRN
          HQPD.K...R..F.F.L.YEDHKTAAQARRRLMSGKVKVWGNVGTVEWADP.EDPDPEVMAKVKVLFVRN
Retrocopy HQPDEKXXXR<TFAF<LKYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPMEDPDPEVMAKVKVLFVRN

Parental  LANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKP
          LANTVTEEILEKAFSQFGKLE.VKKLKDY.FIHFDE.DGAVKAMEEMNGKDLEGENIEIVFAKP
Retrocopy LANTVTEEILEKAFSQFGKLE*VKKLKDYPFIHFDE*DGAVKAMEEMNGKDLEGENIEIVFAKP

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	0.05 RPM	19.75 RPM
SRP007412_cerebellum	0.04 RPM	31.98 RPM
SRP007412_heart	0.12 RPM	44.33 RPM
SRP007412_kidney	0.34 RPM	42.71 RPM
SRP007412_liver	0.10 RPM	40.30 RPM
SRP007412_testis	0.63 RPM	56.49 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1387 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1387 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2410
Pongo abelii	retro_pabe_1775

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018345	1 retrocopy	retro_dnov_1927,
Homo sapiens	ENSG00000135316	1 retrocopy	retro_hsap_2410,
Macaca mulatta	ENSMMUG00000012575	1 retrocopy	retro_mmul_1843,
Nomascus leucogenys	ENSNLEG00000012879	1 retrocopy	retro_nleu_162,
Oryctolagus cuniculus	ENSOCUG00000000601	1 retrocopy	retro_ocun_1683,
Pongo abelii	ENSPPYG00000016819	1 retrocopy	retro_pabe_1775,
Pan troglodytes	ENSPTRG00000000324	1 retrocopy	retro_ptro_474,
Pan troglodytes	ENSPTRG00000018393	1 retrocopy	retro_ptro_1387 ,
Rattus norvegicus	ENSRNOG00000000204	1 retrocopy	retro_rnor_805,
Sus scrofa	ENSSSCG00000004294	1 retrocopy	retro_sscr_436,
Vicugna pacos	ENSVPAG00000001061	1 retrocopy	retro_vpac_391,