RetrogeneDB ID: retro_rnor_1439

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:3783762..3785011(-)
• 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_1439
GGCTATGGGACTCAGTCATCTCCCCAGGGATATGGTTCCACTGGTGGATGGCAGCAGCCCAAGTTCCCAGTGTTCTTATG
GGCACCAGTCCTCCTATCCTGGCTATGGCCAAAAATCAGCTCCTAGCAGCACCTCTGGAAATTATGGTGGCAGTTCTCAG
AGCAGCAGCTATGGGCAGCCCCAGAGCAGAGGCAACAGTCTGGCTATAGTGAACAGCAACAAAGCTCCTAGAACCCACCT
CAGGGTTATGGACAACAGAACCTATACAACAGCAGCAGTGGAGGTGGTAGAGTGGGTGGTGGAGGCAACTAGGGCCAAGA
TCAGTCCTCTATGAGTGGTGGTGGTGGCTGTGGTGGTTACAGCAATCAGGATCAGAGTGATGGCAGTGGTGGTGGCTACA
GGAGTGGCTATGAACCCAACGGCCATGAAGGTGGCAGAGGAGGCAGAGGCAGCATGGGCAGAAGTGACCATGGTGGCTTT
AATAAATTTGGTGGTCCTTGGGATCAAGGATCTCGTCATGATTCTGAACAGGACACTTCAGACAACAATACCATCTTCAT
GCAAGGCCGAGGTGAGAATGTTACAATTGAACCTTTGTCTAATTACTTTAAGCAGATTGGAATTATTAAGACAAACAAGA
AAACTGGACAGCCTATGATTAATTTGTATACAGACAGGGAAACTGGGAATTTGAAGGGTGAGGCAACAGTCTCATTTGTT
AACCTACCTCCTGCTAAAGCTGTAATCGACTAGTTCGATGGTAAATGATTCTCTGTGAATCCTATTAAAGTTTCACTTGC
TACTCACCAAGCTGACATCAATTGGTGTGGTGGAAATGGTTGTGAAGGCTGAGGTTGAGGAGGACACATGGGCCATGGAA
ACTATGGAGGTGGCGGTGGCCAGGGAGGATTCCCCAGTGGGGGAGGTGGAGTTGGAGGACAGTGATGTGCTGGGGACTGG
ATGTGTCCTAATTCTAAATGTGAGAACATGAACTTCCTTTGGAGAAATGAAAGCAAATAGTGTAAGGCACCTAAGCTAGA
TTGTCCAGGAGGGGGACCAGGAGCCTCTCATATGTGGGCAAACTATGGAGATGATCCACAAGACAGAGGAGGATATGATC
AGGGTGTCTAATGGGCAAAAGAGGGGACCTTGGGGTTTTCAAAGGGGGCCTGGTGGTGCAGACAGAAGTGGATTTGTCCC
TGGCAAGATGGACTCCATGGCTGAGCCCAGACAGGATCACCATGACAGG

Alignment

ORF - retro_rnor_1439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.86 %
• Parental protein coverage: 80.5 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GYGQQPAPSSTSGSYG-GSSQSS--SYGQPQS-GGYGQQSGYGGQQQSYG--QQQSSYNPPQGYG-QQNQ
          GYG.Q..P.......G.GSS.SS..SYG...S..GYGQ.S........YG...Q.SSY..PQ..G.QQ..
Retrocopy GYGTQSSPQGYGSTGG>GSSPSSQCSYGHQSSYPGYGQKSAPSSTSGNYGGSSQSSSYGQPQSRG<QQSG

Parental  YNSSSGGGGGGGGGNYGQDQ--SSMSGGG--GGGGYGNQDQSGGGGGGYGGGQQDRGGRGRGGGGGYNRS
          Y............G.YGQ.....S.SGGG..GGGG...QDQS...GGG..GG.........G.GGGY...
Retrocopy YSEQQQSS*NPPQG-YGQQNLYNSSSGGGRVGGGGN*GQDQSSMSGGGGCGGYSNQD-QSDGSGGGYR--

Parental  SGGYEPRGRGGGRGGRGGMGGSDRGGFNKFGGPRDQGSRHDSEQDNSDNNTIFVQGLGENVTIESVADYF
          ..GYEP.G..GGRGGRG.MG.SD.GGFNKFGGP.DQGSRHDSEQD.SDNNTIF.QG.GENVTIE....YF
Retrocopy -SGYEPNGHEGGRGGRGSMGRSDHGGFNKFGGPWDQGSRHDSEQDTSDNNTIFMQGRGENVTIEPLSNYF

Parental  KQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF
          KQIGIIKTNKKTGQPMINLYTDRETG.LKGEATVSF...P.AKA.ID.FDGK.FS.NPIKVS.AT..AD.
Retrocopy KQIGIIKTNKKTGQPMINLYTDRETGNLKGEATVSFVNLPPAKAVID*FDGK*FSVNPIKVSLATHQADI

Parental  NRGGGNGRGGRGRGGPMGRGGYGGGGSGGGGRGGFPSGGGGGGGQQRAGDWKCPNPTCENMNFSWRSECN
          N..GGNG..G.G.GG.MG.G.YGGGG....G.GGFPSGGGG.GGQ..AGDW.CPN..CENMNF.WR.E..
Retrocopy NWCGGNGCEG*G*GGHMGHGNYGGGG----GQGGFPSGGGGVGGQ*CAGDWMCPNSKCENMNFLWRNESK

Parental  QCKAPKPDGPGGGPGGSHMGGNYGDDRRGRGGYDR-GGYRGRGGDRG-GFRGGRGGGDRGGFGPGKMDSR
          .CKAPK.D.PGGGPG.SHM..NYGDD...RGGYD..G...G..GD.G.GF..G.GG.DR.GF.PGKMDS.
Retrocopy *CKAPKLDCPGGGPGASHMWANYGDDPQDRGGYDQ<GCLMGKRGDLG<GFQRGPGGADRSGFVPGKMDSM

Parental  GEHRQDRRER
          .E.RQD...R
Retrocopy AEPRQDHHDR

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	0.00 RPM	51.17 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1439 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1439 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,