RetrogeneDB ID: retro_rnor_913

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:49670880..49672064(+)
• Located in intron of: ENSRNOG00000003953

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fus
• Ensembl ID: ENSRNOG00000023360
• Aliases: None
• Description: RNA-binding protein FUS [Source:RefSeq peptide;Acc:NP_001012137]

Sequence

>retro_rnor_913
CAGGCAGCTCATAGCTATGGAGCCTATCCTACCCAGCCTGGGCAGGGCTGTTCCCAACAGAGCCATCAGCCCTATGGCCA
GCAGAGTTACAGTGGTTATGGCCAATCAGCTGACACTTCAGGATATGGTCACAGCAGCTCTGGTTCTTCTTATGGACAGA
CCCAAAACAGCTATGGAACTCAGTCAGCTCCCCAGGGATAGGGTTCCACTGGTGGCCATGGCAGCAGCCAAAGTTCCCAG
CCTTCTTATGAGCAGCAGCCCTCCTACCCCGGCTATGGCCAACAGCCAGCTACTAGTAGCACCTCAGGAAATTATGGTGG
CAGTTCTCAGAGCAGCAGCTGTGGGCAGCCCCAGAGCGGAGGCCATGGTCAACAATCTGGCTATGGTGGACAGCAACAAA
GCTCCTATGACCCACCTCAGGGCTCTGGACAGCAGAGCCAGTACAACAGCAGCAGTGGAGGGGTGGAGGGGGTGGTGGAG
GCGACTGTGGCCAAGATCAGTCCTCTATGAGTGCTGGCCGTGGTGGCTATGGGGGAGGCCAGCAGGATGGTGGGGGCCGT
GGCTGGGGCGGTGGAGGTGGCACAAGTGACGTAGTGGTGGCTATGAACTCAGAGCCCGGGAGGTAGTGGAGGAGGCACAG
GCAGGGTGGGTGCAAGTGACCATGGTGGCTTCGAAGATTTTGGTGTCCTCTGGATCAAGTATCTTGTCATGATTCCGAAA
AGGGTAATTCAGACAATACCATCTCTGTGCAAGGTCTAGGTGAGAATGCTACAAGTGAATCTGTGGCCGATTACGTCAAG
CAGATTGAAATTATTAAGGCAAACAGGAAAACTGGACAGCCTATGATTGATTTGTGTACAGACAGGGAAACCGGCAAGTT
GAAGGGTGAGGCAGCAGTCTCCTTTGGTGACCCCCATCTGCTAAAGCTGCAATCGACTGGTTTGATGTTAAAGAATTCTC
TGGGAATCCATTAAAGTTTCTCCTGCTACCCGGCGTGCTGACTTCAACCAGGGTGGTGGAAATGGTCATGGAGGCCGAGT
TCGAGGAGGACCCATAAGCCTTGGAGGCTATGGAGGAGGTGGCAGCAGTAGCCGGGGAGGATTCCCCAGTGAAGGTGGTG
GAGATGGAGGACAGGAACGAGCTGGGGACTAGAAGTTCCTAATCCTACATGTTAGAACATGAGC

Alignment

ORF - retro_rnor_913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.37 %
• Parental protein coverage: 74.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  QSADTSGYGQSSYGSSYGQTQNTGYGTQSAPQGYGS---TGGYGSSQSSQSSYGQQSSYPGYGQQPAPSS
          Q.A...G......G....Q.....YG.QS...GYG....T.GYG.S.SS.SSYGQ......YG.Q.AP..
Retrocopy QAAHSYGAYPTQPGQGCSQQSHQPYGQQSY-SGYGQSADTSGYGHS-SSGSSYGQTQN--SYGTQSAPQG

Parental  --TSGSYGGS--SQSSSYGQPQSGGYGQQSGYGGQQQSYG--QQQSSYNPPQ--GYGQQNQYNSSSGGGG
          ....G..G.S..SQ.S...QP...GYGQQ.........YG...Q.SS...PQ..G.GQQ..Y........
Retrocopy *GSTGGHGSSQSSQPSYEQQPSYPGYGQQPATSSTSGNYGGSSQSSSCGQPQSGGHGQQSGYGGQQQSSY

Parental  GGGGGNYGQDQ-SSMSGG-GGGGGYGN--QDQS--GGGGGGYGGGQQDRGGRGRGGGGG-YNRSSGGYEP
          ....G...Q.Q..S.SGG.GGGGG.G...QDQS....G.GGYGGGQQD.GGRG.GGGGG.....SGGYE.
Retrocopy DPPQGSGQQSQYNSSSGG<GGGGGGGDCGQDQSSMSAGRGGYGGGQQDGGGRGWGGGGG<HK*RSGGYEL

Parental  RGR-GGGRGGRGGMGGSDRGGFNKFG-GPRDQGSRHDSEQDNSDNNTIFVQGLGENVTIESVADYFKQIG
          R.R.GG..GG.G..G.SD.GGF..FG..P.DQ.S.HDSE..NSD.NTI.VQGLGEN.T.ESVADY.KQI.
Retrocopy RAR<GGSGGGTGRVGASDHGGFEDFG<CPLDQVSCHDSEKGNSD-NTISVQGLGENATSESVADYVKQIE

Parental  IIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD-PPSAKAAIDWFDGKEFSGNP-IKVSFATRRADFNR
          IIK.N.KTGQPMI.L.TDRETGKLKGEA.VSF.D.PPSAKAAIDWFD.KEFSGNP.IKVS.ATRRADFN.
Retrocopy IIKANRKTGQPMIDLCTDRETGKLKGEAAVSFGD<PPSAKAAIDWFDVKEFSGNP<IKVSPATRRADFNQ

Parental  GGGNGRGGRGRGGPMGRGGYGGGGSGGGGRGGFPSGGGGGGGQQRAGDWK-CPNPTCENMN
          GGGNG.GGR.RGGP...GGYGGGGS....RGGFPS.GGG.GGQ.RAGD.K..PNPTC.NM.
Retrocopy GGGNGHGGRVRGGPISLGGYGGGGS--SSRGGFPSEGGGDGGQERAGD*K<VPNPTC*NMS

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	118.63 RPM
SRP017611_kidney	0.00 RPM	70.90 RPM
SRP017611_liver	0.07 RPM	51.17 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_913 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_913 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_913 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000000968	1 retrocopy	retro_meug_1986,
Myotis lucifugus	ENSMLUG00000004806	3 retrocopies	retro_mluc_1934, retro_mluc_608, retro_mluc_638,
Macaca mulatta	ENSMMUG00000019637	1 retrocopy	retro_mmul_153,
Mus musculus	ENSMUSG00000030795	2 retrocopies	retro_mmus_2710, retro_mmus_2952,
Rattus norvegicus	ENSRNOG00000023360	4 retrocopies	retro_rnor_1439, retro_rnor_2727, retro_rnor_2894, retro_rnor_913 ,