RetrogeneDB ID: retro_rnor_2727

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:38568844..38570344(-)
• Located in intron of: None

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_2727
ATGGCTTCAAACGACTATATCCAACAAGCAACTCAAAGCTATGGGACCTATCCTACCCAGCCTGGGCAGGGCTATTCCCA
ACAGAGCAATCAGCCCTATGACCAGCAGAGTTAAGTGGTTATGGCCAAACCGCTGATACTTCAAGATACGGCCAGAGCAG
CTATGGTTCTTCTTATGGACAGACCCAAAACAGCTATGGAACTCAGTCAGCTCTCCAGGGATAGGGTTCCCCTGGTGGCT
ATGGCAGCAGCCAAAGTTCCCAGCCTTCTTATGGGCAGCAGTCCTCCTACCCCGGCTATGGCCAACAGCCAGCTCCTAGC
AGCACCTCAGGAAGTTATGATGGAGTTCTCAGAGCAGCAGCTATGGGCAGCCCCAAAATGGAAGCTATGGTCAACAGTCT
GCCTATGGTGGATAGCAACAAAGCTCCTATAACCCACCTCAGGGTTATGGAGAACAGAACCAGTACAACAGCAGCAGTGG
AGGTGGTGGAGGCAACTATGGCCAACATCAGTCCTCTATGAGTGGCGGTGGCAGTGGCGGGGGTGGTTATGGCAATCAGG
ACCAGAGTGGTGGCGGCGGTGGGTGGTGGCTACGGGGGAGGCCTATAGGATCGTGGGGGTCGTGGCAAGGGCGGTGGAGG
TGGTTACAACTGAAGCAGTGGTGGCTATGAACCCAGAGGCTGTGGAGGTGGCTGAGGAGGCAGAGGCAACACGGGCGAAA
GTGACCATGGTGGCTTCAATAAATTTGGTCATCCTCGGGATCAAGGATCTCGTCATGATTATAAACAGGATAATTCAGAC
AACAATACCATCTTCGTGCAAGGCCTAGGCGAAATGTTACAATTGAGTCTGTGGCAGATTACTTCAAGCAGATTGGAATT
ATTAAGACAAACAAGAAAACTGGACAGCCTATGATTAATTTGTATACAGACAGGGAAACTGGCAAGTTGAAGGGTGAGGC
AACATCTCATTTGATGACCCACCTTCTACTAAAGCTGCAATCGACTGGTTTGATGGTAAAGAATTCTCTGGGAATCCTAT
TAAAGTTTCATTTGCTACCCAAAGTGCTGATTTCAACCGGGGTGGTAGAAGTGGTTGTGGAGGCCGAGGGCGAGGAGGAC
CCATGGGCTGTGGAGGCTATGGAGGAGGTGGCAGCAGTGGTGGTGGCCGGGGAGGATTCCCCAGTGGAGGTGGTGGAGGT
GGAGGACAGCAACGAGCTGGGGACTGGAAGTGTCCTAATCCTACATGTGAGAACATGAACTTCTCTTGGAGAAATGAATG
CAACCAGTGTAAGGCACCTAAGCCAGATGGCCCAGGATGGGGACCAGGAGGCTCTCATGTTGGGAGAAACTACAAAGATG
ACCGACAGGGCAGAGGAGGATATGATCGGGCCGGCTACCAGGGCTGAGGAGGGGACCGTGGGGGCTTCAGAGGGGGCCGG
GGTGGTGGGGACAGAGGTGGTTTTGGCCTTGGCAAGATGGACTCCAGGGGTGAGCACAGA

Alignment

ORF - retro_rnor_2727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.62 %
• Parental protein coverage: 98.46 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MASNDYTQQATQSYGAYPTQPGQGYSQQSNQPYGQQS-YSGYGQSADTSGYGQSSYGSSYGQTQNTGYGT
          MASNDY.QQATQSYG.YPTQPGQGYSQQSNQPY.QQS..SGYGQ.ADTS.YGQSSYGSSYGQTQN..YGT
Retrocopy MASNDYIQQATQSYGTYPTQPGQGYSQQSNQPYDQQS<LSGYGQTADTSRYGQSSYGSSYGQTQNS-YGT

Parental  QSAPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGG-SSQSSSYGQPQSGGYGQQSGYG
          QSA.QG.GS.GGYGSSQSSQ.SYGQQSSYPGYGQQPAPSSTSGSY.G.SSQSSSYGQPQ.G.YGQQS.YG
Retrocopy QSALQG*GSPGGYGSSQSSQPSYGQQSSYPGYGQQPAPSSTSGSYDG<SSQSSSYGQPQNGSYGQQSAYG

Parental  GQQQSYGQQQSSYNPPQGYGQQNQYNSSSGGGGGGGGGNYGQDQSSMSGGGGGGGYGNQDQSGGGG-GGY
          G.QQS.......Y....G...Q....S..GGG..G.........S....GG..GGYGNQDQSGGGG.GG.
Retrocopy G*QQSSYNPPQGY----GEQNQYNSSSGGGGGNYG---QHQSSMSGGGSGG--GGYGNQDQSGGGG>GGG

Parental  GGGQQDRGGRGRGGG-GGYNRSSGGYEPRGRGGGRGGRGGMGGSDRGGFNKFGGPRDQGSRHDSEQDNSD
          .GG.....G....GG.GGYN.SSGGYEPRG.GGG.GGRG..G.SD.GGFNKFG.PRDQGSRHD..QDNSD
Retrocopy YGGGL*DRGGRGKGGGGGYN*SSGGYEPRGCGGG*GGRGNTGESDHGGFNKFGHPRDQGSRHDYKQDNSD

Parental  NNTIFVQGLGE-NVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT-VSFDDPPSAKAAI
          NNTIFVQGLGE.NVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT..SFDDPPS.KAAI
Retrocopy NNTIFVQGLGE<NVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT<ISFDDPPSTKAAI

Parental  DWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGRGRGGPMGRGGYGGGGSGGGGRGGFPSGGGGGGGQQ
          DWFDGKEFSGNPIKVSFAT..ADFNRGG..G.GGRGRGGPMG.GGYGGGGS.GGGRGGFPSGGGGGGGQQ
Retrocopy DWFDGKEFSGNPIKVSFATQSADFNRGGRSGCGGRGRGGPMGCGGYGGGGSSGGGRGGFPSGGGGGGGQQ

Parental  RAGDWKCPNPTCENMNFSWRSECNQCKAPKPDGPGGGPGGSHMGGNYGDDRRGRGGYDRGGYRGRGGDRG
          RAGDWKCPNPTCENMNFSWR.ECNQCKAPKPDGPG.GPGGSH.G.NY.DDR.GRGGYDR.GY.G.GGDRG
Retrocopy RAGDWKCPNPTCENMNFSWRNECNQCKAPKPDGPGWGPGGSHVGRNYKDDRQGRGGYDRAGYQG*GGDRG

Parental  GFRGGRGGGDRGGFGPGKMDSRGEHR
          GFRGGRGGGDRGGFG.GKMDSRGEHR
Retrocopy GFRGGRGGGDRGGFGLGKMDSRGEHR

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	0.22 RPM	118.63 RPM
SRP017611_kidney	0.21 RPM	70.90 RPM
SRP017611_liver	0.13 RPM	51.17 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2727 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2727 has 0 orthologous retrocopies within eutheria group .

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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,