RetrogeneDB ID: retro_rnor_2894

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:16736506..16737916(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000028611
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2894
ATGGCTTCAAACGACTATACCCAACAAGCAACTCAAAGCTATGGGGCCTATCCTACCCAGCCTGGGCAGGGCTATTCCCA
ACAGAGCAATCAGCCCTATGGCCAGCAGAGTTACAGTGGTTATGGCCAATCAGCTGACACTTCAGGATACGGCCAGAGCA
GCTATGGTTCTTCTTATGAACAGACCCAAAACACAGGCTATGGAACTCAGTCAGCTCCCCAGGGATATGGTTCCACTGGT
GGCTATGGCAGCAGCCAAAGTTCCCAGTCTTCTTATGGGCAGCAGTCCTCCTACCCCGGTTATGGCCAACAGCCAGCTCC
TAGTAGCACCTCAGGAAGTTATGGTGGCAGTTCTCAGAGCAGCAGCTATGGGCAGCCCCAGAGTGGAGGCTATGGTCAAC
AGTCTGGCTATGGTGGACAGCAACAAAGCTACGGACAGCAACAAAGCTCCTATAACCCACCTCAGGGTTATGGACAACAG
AACCAGTACAACAGCAGGCAGTGGAGGTGGTGGAGGGGTGGTGGAGGCAACTATGGCCAAGATCAGTCCTCTATGAGTGG
CGGCGATGGCGGTGGTGGTTATGGCAATCAGTACCAGAGTGGTGGCAGCGGTGGTGGCTACGGGGGAGGCCAGCAGGATC
GTGGGGGCCATGGCAGGGGCGGTGGAGGTGTTTACAACCGAAGCAGTGGTGGCTATGAACCCAGAGGCCGTGGAGGTGGC
CGAGGAGGCAGAGGCGGCATGGGCGGAAGTGACCGTGGTGGCTTCAATAAATTTGGTGGTCCTCGGGATCAAGGATCTCA
TCATGATTCTGAACAGGATAATTCAGACAATAATACCATCTTCGTGCAAGGCCTAGGCGAGAATGTTACAATTGAATCTG
TGGCGGATTACTTCAAGCAGATTGGAATTATTAAGACAAACGAGAAAACTGGACAGCCTATGATTAATTTGTATACAGAC
AGGGAAACTGGCAAGTTGAAGGGTGAGGCAACAGTCTCATTTGATGACCCACCTTCTGCTAAAACTGCAATCGACTGGTT
TGATGGAAAAGAATTCTCTGGGAATCTTATTAAAGTTTCATTTGCTACCCGGCGTGCTGACTTCAACCGGGTAAATGGTC
GTGGAGGCCGAGGGCAAGGAGGACCCATGGGCCATGGAGGCTATGGAGGAGGTGGCAGCGGTGGTGGTGGCCGGGGAGGA
TTCCCCAGTGGAGGTGGTGGAGGTGGAGGACAGCAACGAGCTGGGGACTGGAAGTGTCCTAATCCTACATGTGAGAACAT
GAACTTCTCTTGGAGAAGTGAATGCAACCAGTGTAAGGCACCTAAGCCAGATGGCCCAGGAGGGGGACCAGGAGGCTCTC
ATATGGGGGGAAACTACGGTGATGATCGGCATGGCAGAGGAGGATATGAT

Alignment

ORF - retro_rnor_2894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.99 %
• Parental protein coverage: 91.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASNDYTQQATQSYGAYPTQPGQGYSQQSNQPYGQQSYSGYGQSADTSGYGQSSYGSSYGQTQNTGYGTQ
          MASNDYTQQATQSYGAYPTQPGQGYSQQSNQPYGQQSYSGYGQSADTSGYGQSSYGSSY.QTQNTGYGTQ
Retrocopy MASNDYTQQATQSYGAYPTQPGQGYSQQSNQPYGQQSYSGYGQSADTSGYGQSSYGSSYEQTQNTGYGTQ

Parental  SAPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGGSSQSSSYGQPQSGGYGQQSGYGGQ
          SAPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGGSSQSSSYGQPQSGGYGQQSGYGGQ
Retrocopy SAPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGGSSQSSSYGQPQSGGYGQQSGYGGQ

Parental  QQSYGQQQSSYNPPQGYGQQNQYNS-SSGGGGG-GGGGNYGQDQSSMSGGGGGGGYGNQDQSGGGGGGYG
          QQSYGQQQSSYNPPQGYGQQNQYNS..SGGGGG.GGGGNYGQDQSSMSGG.GGGGYGNQ.QSGG.GGGYG
Retrocopy QQSYGQQQSSYNPPQGYGQQNQYNS>GSGGGGG<GGGGNYGQDQSSMSGGDGGGGYGNQYQSGGSGGGYG

Parental  GGQQDRGGRGRGGGGGYNRSSGGYEPRGRGGGRGGRGGMGGSDRGGFNKFGGPRDQGSRHDSEQDNSDNN
          GGQQDRGG.GRGGGG.YNRSSGGYEPRGRGGGRGGRGGMGGSDRGGFNKFGGPRDQGS.HDSEQDNSDNN
Retrocopy GGQQDRGGHGRGGGGVYNRSSGGYEPRGRGGGRGGRGGMGGSDRGGFNKFGGPRDQGSHHDSEQDNSDNN

Parental  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD
          TIFVQGLGENVTIESVADYFKQIGIIKTN.KTGQPMINLYTDRETGKLKGEATVSFDDPPSAK.AIDWFD
Retrocopy TIFVQGLGENVTIESVADYFKQIGIIKTNEKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKTAIDWFD

Parental  GKEFSGNPIKVSFATRRADFNRGGGNGRGGRGRGGPMGRGGYGGGGSGGGGRGGFPSGGGGGGGQQRAGD
          GKEFSGN.IKVSFATRRADFNR...NGRGGRG.GGPMG.GGYGGGGSGGGGRGGFPSGGGGGGGQQRAGD
Retrocopy GKEFSGNLIKVSFATRRADFNR--VNGRGGRGQGGPMGHGGYGGGGSGGGGRGGFPSGGGGGGGQQRAGD

Parental  WKCPNPTCENMNFSWRSECNQCKAPKPDGPGGGPGGSHMGGNYGDDRRGRGGYD
          WKCPNPTCENMNFSWRSECNQCKAPKPDGPGGGPGGSHMGGNYGDDR.GRGGYD
Retrocopy WKCPNPTCENMNFSWRSECNQCKAPKPDGPGGGPGGSHMGGNYGDDRHGRGGYD

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	0.36 RPM	118.63 RPM
SRP017611_kidney	0.21 RPM	70.90 RPM
SRP017611_liver	0.34 RPM	51.17 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2894 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2894 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,