RetrogeneDB ID: retro_pabe_1775

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:698704..700248(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNCRIP
• Ensembl ID: ENSPPYG00000016819
• Aliases: None
• Description: synaptotagmin binding, cytoplasmic RNA interacting protein [Source:HGNC Symbol;Acc:16918]

Sequence

>retro_pabe_1775
ATTTACGTTGCAGGGCTAGTTGCACGTAGTGATTTAGATAAAAGAACTATCGAAGCTTTAAAAGAATTCAATGAAGACGG
TGCATTGGCAGTTCTTCAACATTTAAAGACAGTGATCTCATGTTCAGAACAAAAGTGCCTTTTTATGTGGAGTCATGAAG
ACTTACAGGCAGAGAGAAAAACAAGGGACCAAAGTAGCAGATTCTAGTAAAGGACCAGATGAGGCAAAAATTAAGGCACT
CTTGGAAAGAACAGGCTACACACTTGATGTGATCACTGGACAGAGGAAGTATGGAGGACCACCTCCAGATTCCGTTTATT
CAGGTCAGCAGCCTTCTGTTGGCACTGAGATATTTGTGGGAAAGATCCCAAGAGATCTATTTGAGGATGAACTTGTTCCG
TTATTTGAGAAAGCTGGACCTATATGGGATCTTCGTCTAATGATGGAGCCACTCACTGGTCTCAATAGAGGTTATGCATT
TGTCACTTTTTGTACAAAAGAAACAGCTCAGGAGGCTGTTAAACTGTATGATAATCATGAAATTCGTTCTGGAAAACACA
TTGGTGTCTGCATCTCAGTTGCCAACAATAGGCTTTTTGTGGGCTCTATTCCTAAGAGTAAAACCAAGGAACAGATTCTT
GAAGAATTTAGCAAAGTAACAGAGAGTCTTACAGACTTCATTTTATACCACCAACCGGATGACAAGAAAAAAAACAGGCT
TTTGCTTTCTTGATATGAAGATCACAAAACAGCTGCCCAGGCAAGGCGTAGGTTAATGAGTGATAAAGTCAAGTTCTGGG
GGAATGTTGGAACCGTTGAATGGGCTGGTCCTATGGAAGGTCCTGATCCTGAGGTTATGGCAAAGGTAAAAGTGCTGTTT
GTACGCAACCTTGCCAATACTGTAACAGAAGAGATTTTAGAAAAGGCATTTAGTCAGTTTGGGAAACTGGAACGAGTGAA
GAAGTTAAAAGATTATGCATTCATTCATTTTGATGAGTGAGCGGGCGCTGTCAAAGCTATGGAAGAAATGAATGGCAAAG
ACTTGGAGGGAGAAAATATTGAAATTGTTTTTGCCAAGCCACTAGATCAGAAAAGGAAAGAAAGAAAAGCTCAGAGGCAA
GCAGCAAAAAATCAAATGTATGACGATTACTACTATTATGGTCCACCTTATATGCCCCCTCCAACAAGAGATCGAGGGCA
TGGAGGTAGAGGTGGTTATAGATATCCTCTCCANATGATTTGGATATGAAGATTATTATGATTATTATGGCTATGATTAC
CATAACTATCGTGGTGGATATGAAGATCCATACTATGGTTATGAAGATTTTCAAGTTGGAGCTAGAGGAAGGGGTGGTAG
AGGAGCAAGGGGTGCTGCTCCATCCAGAGGTCGTGGGGCTGCTCCTCCCTGCAGTAGAGCCGGTTATTCACAGAGAGGAG
GTCTTGGATCAGCAAGAGGCGTTTGAGGTGCGAGAGGAGGTGCCCAACAACAAAGAGGCCAGGGGCAGGGAAAAGGGGTC
GAGGCTGGTCCTGACCTGTTGGAA

Alignment

ORF - retro_pabe_1775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.58 %
• Parental protein coverage: 91.99 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IYVAGLVAHSDLDERAIEALKEFNEDGALAVLQQ-FKDSDLSHVQNKSAFLCGVMKTYRQREKQGTK-VA
          IYVAGLVA.SDLD.R.IEALKEFNEDGALAVLQ..FKDSDL...............T.R...K.G.K.VA
Retrocopy IYVAGLVARSDLDKRTIEALKEFNEDGALAVLQH<FKDSDLMFRTKVPFYVES*RLTGREKNK-GPK<VA

Parental  DSSKGPDEAKIKALLERTGYTLDVTTGQRKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFE
          DSSKGPDEAKIKALLERTGYTLDV.TGQRKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFE
Retrocopy DSSKGPDEAKIKALLERTGYTLDVITGQRKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFE

Parental  KAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLYNNHEIRSGKHIGVCISVANNRLFVGSIPKS
          KAGPIWDLRLMM.PLTGLNRGYAFVTFCTKE.AQEAVKLY.NHEIRSGKHIGVCISVANNRLFVGSIPKS
Retrocopy KAGPIWDLRLMMEPLTGLNRGYAFVTFCTKETAQEAVKLYDNHEIRSGKHIGVCISVANNRLFVGSIPKS

Parental  KTKEQILEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWA
          KTKEQILEEFSKVTE.LTD.ILYHQPDDK...R............A...RR.LMS.KVK.WGNVGTVEWA
Retrocopy KTKEQILEEFSKVTESLTDFILYHQPDDKXXXRLLLS*YEDHKTAAQARRR-LMSDKVKFWGNVGTVEWA

Parental  DPIEDPDPEVMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNG
          .P.E.PDPEVMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDE..GAVKAMEEMNG
Retrocopy GPMEGPDPEVMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDE*AGAVKAMEEMNG

Parental  KDLEGENIEIVFAKPPDQKRKERKAQRQAAKNQMYDDYYYYGPPHMPPPTRGRGRGGRGGYGYPPDY-YG
          KDLEGENIEIVFAKP.DQKRKERKAQRQAAKNQMYDDYYYYGPP.MPPPTR.RG.GGRGGY.YP.....G
Retrocopy KDLEGENIEIVFAKPLDQKRKERKAQRQAAKNQMYDDYYYYGPPYMPPPTRDRGHGGRGGYRYPLXM>FG

Parental  YEDYYDYYGYDYHNYRGGYEDPYYGYEDFQVGARGRGGRGARGAAPSRGRGAAPPRGRAGYSQRGGPGSA
          YEDYYDYYGYDYHNYRGGYEDPYYGYEDFQVGARGRGGRGARGAAPSRGRGAAPP..RAGYSQRGG.GSA
Retrocopy YEDYYDYYGYDYHNYRGGYEDPYYGYEDFQVGARGRGGRGARGAAPSRGRGAAPPCSRAGYSQRGGLGSA

Parental  RGVRGARGGAQQQRGRGQGKGVEAGPDLLQ
          RGV.GARGGAQQQRG.GQGKGVEAGPDLL.
Retrocopy RGV*GARGGAQQQRGQGQGKGVEAGPDLLE

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	24.55 RPM
SRP007412_cerebellum	0.00 RPM	28.58 RPM
SRP007412_heart	0.06 RPM	35.16 RPM
SRP007412_kidney	0.07 RPM	44.45 RPM
SRP007412_liver	0.06 RPM	42.20 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1775 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1775 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1775 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2410
Pan troglodytes	retro_ptro_1387

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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	ENSPPYG00000015863	1 retrocopy	retro_pabe_1502,
Pongo abelii	ENSPPYG00000016819	1 retrocopy	retro_pabe_1775 ,
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,