RetrogeneDB ID: retro_rnor_805

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:64952913..64953811(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Syncrip
• Ensembl ID: ENSRNOG00000000204
• Aliases: None
• Description: Heterogeneous nuclear ribonucleoprotein Q [Source:UniProtKB/Swiss-Prot;Acc:Q7TP47]

Sequence

>retro_rnor_805
TCCGTTTTCAAGAGTAAAACCAAGAAACATATTCTTGAAGAGTTTAGTAAAGCAATCCAGGGTCTCACAGCCCTCATTTT
ACATTCCCAACTAGATGACAAGAAAAAAAAAGAGGCTTTTGCTTTCTTCAATATGAAGATTGCAAAATAGCTGCCAAGAC
AAAGTGCATGTTAATGAGTGATAAAGCCAAAGTCTGGGAGAATGTGGGGACTGTTGAATGGGCTGGTTCTATTGTCTACG
CTGAAGTTATAGCAAAGGTAAAAGTGCTGTTAGTAGGCTATCTTGCCAATAATGTAACAGAAGAAATTTTAGAAACACTG
TTTATTCAGTTTGGGGAACTGGAACAAGTGAAAAAGCTAAAACATTATGCTTTCAGACATTTTGAAGCACAAGACAGTGT
TGTCAAGGCTATGGAAGAAATGAATGCTAAATACTTGGAGAGACAAAAATATTGAACTTGTTTTTGCTGAGTTATGAGAT
CACTCAGCTCATAGGCAAATAGCAAAGAATCAAATGTATGACAATTACTACTATTATGGGTCCTTGTATATGATCCTTCC
CCAACAAGAGGTCAAGGGCATGGAAGTAAAAGTGGCTATGGGTATCCTCCAGATTATTATGGATATAAAATAATTATGAT
CATTATGGCTGTGGTTACTATAACTATCATAGTGTATAGGAAGATCTATACTATGATTATGAAGAGTTTCAAGTTGGAGC
TATAGGAAGGGATCATAGAGGAACAAAAGGTGCTGCTCCATCCAGAGGTTTTGGGGATGCTCCTCCCCATGGTAGGGCCA
GTTATTCACAAAGGAGAGTCTCTGGATCCGCAAAAGGCATTTATGGTACAAGAGAAAGTGCCCAGAAACAAAAAGAATAA
GGAGGAAAGGGGGTCAAG

Alignment

ORF - retro_rnor_805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.13 %
• Parental protein coverage: 59.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SIPKSKTKEQILEEFSKVTEGLTDVILYHQPDDKKKNR-GFCFLEYEDHKTAAQARRRLMSGKVKVWGNV
          S..KSKTK..ILEEFSK...GLT..IL..Q.DDK.....GFCFL.YED.K.AA.....LMS.K.KVW.NV
Retrocopy SVFKSKTKKHILEEFSKAIQGLTALILHSQLDDKXXXE<GFCFLQYEDCKIAAKTKCMLMSDKAKVWENV

Parental  GTVEWADPIEDPDPEVMAKVKVLFVRNLANTVTEEILEKSFSQFGKLERVKKLKDYAFIHFDERDGAVKA
          GTVEWA..I......V.AKVKVL.V..LAN.VTEEILE..F.QFG.LE.VKKLK.YAF.HF...D..VKA
Retrocopy GTVEWAGSIVYAE--VIAKVKVLLVGYLANNVTEEILETLFIQFGELEQVKKLKHYAFRHFEAQDSVVKA

Parental  MEEMNGKDLE-GENIEIVFAKPPDQKRKERKAQRQAAKNQMYDDYYY-YGPPHMPPPTRGRGRGGRGGYG
          MEEMN.K.LE...NIE.VFA...D.......A..Q...N..Y....Y.Y.P...P....G.G.....GYG
Retrocopy MEEMNAKYLE>DKNIELVFAEL*DHSAHRQIAKNQMYDNYYYYGSLY<YDP--SPTRGQGHG--SKSGYG

Parental  YPPDYYGYE-DYYDYYGYDYHNYRGGYEDPYYGYEDFQVGARGRGGRGARGAAPSRGRGAAPPRGRAGYS
          YPPDYYGY....YD.YG..Y.NY....ED.YY.YE.FQVGA.GR..RG..GAAPSRG.G.APP.GRA.YS
Retrocopy YPPDYYGYK<NNYDHYGCGYYNYHSV*EDLYYDYEEFQVGAIGRDHRGTKGAAPSRGFGDAPPHGRASYS

Parental  QRGGPGSARGVRGARGGAQQQRGRGVRGAR
          QR...GSA.G..G.R..AQ.Q...G..G..
Retrocopy QRRVSGSAKGIYGTRESAQKQKE*GGKGVK

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
SRP017611_brain	0.00 RPM	18.55 RPM
SRP017611_kidney	0.00 RPM	26.59 RPM
SRP017611_liver	0.00 RPM	17.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_805 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_805 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_805 has 0 orthologous retrocopies within eutheria group .

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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	ENSPTRG00000018393	1 retrocopy	retro_ptro_1387,
Rattus norvegicus	ENSRNOG00000000204	1 retrocopy	retro_rnor_805 ,
Rattus norvegicus	ENSRNOG00000016894	1 retrocopy	retro_rnor_2782,
Sus scrofa	ENSSSCG00000004294	1 retrocopy	retro_sscr_436,
Vicugna pacos	ENSVPAG00000001061	1 retrocopy	retro_vpac_391,