RetrogeneDB ID: retro_rnor_2136

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:29725801..29726467(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Wsb1
• Ensembl ID: ENSRNOG00000012929
• Aliases: None
• Description: WD repeat and SOCS box-containing 1 isoform 1 [Source:RefSeq peptide;Acc:NP_001036026]

Sequence

>retro_rnor_2136
ATGGCCAGCTTTCCCCCAAGGGACAACGAGAAAGAGATCGTGAGGTCGCGCACTATAGAAGAACTTTCAACTCCAGCAGC
CCCTTTCGACAGGAAATGTGGTGGTGAAAACTGGACTGTTGCTTTTGCTCCAGATGGTTCATACTTTGCATGGTCACTAG
GATTTCATATAGTGAAGCTTGTCCTGTGGTCCCGGTGCCTTAAGAACTTTCTTTTGCATGGTTCCAAGAATGTTACCAAT
TCAAGCTGTCTAAAATTGGCAAGACAAAATAGTAATGGTGCTCAAAAAAATAAGCCCCGTGAACACGTTATAGACTGTGG
AGACATAGTCTGGAGTCTCGCTTTTGGGTCTTCAGTTCCAGAAAAACAGAGTCGTTGTGTTAATAGAGAATGGCATCGGT
TTTGATTTGGACAGGATCAGCTACTCCTTGCCACAGGATTAAATAATGGTCGCATCAAAATCTGGGATGTGTATACAGGA
AAACTCTTCCTTGATTTGGCAGACCACATTGAAGTGGTTAGAGACTTAACTTTCGCTCCAGGTGGGAGCTTACTCCTTTT
ATCAGCTTCAAGAGACAATATTCTTAGAGTGTGGGACCTGAAAGGTGATGGAAATATGAGTATTGTGGGGCCATCAGAAT
TGGGTGTACAGTTGTGCGTTTTCTCC

Alignment

ORF - retro_rnor_2136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.3 %
• Parental protein coverage: 52.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASFPPRVNEKEIVRSRTIGELLAPAAPFDKKCGGENWTVAFAPDGSYFAWSQGYRIVKLVPWSQCLKNF
          MASFPPR.NEKEIVRSRTI.EL..PAAPFD.KCGGENWTVAFAPDGSYFAWS.G..IVKLV.WS.CLKNF
Retrocopy MASFPPRDNEKEIVRSRTIEELSTPAAPFDRKCGGENWTVAFAPDGSYFAWSLGFHIVKLVLWSRCLKNF

Parental  LLHGSKNVTNSSCLKLARQNSNGGQKNKPREHIIDCGDIVWSLAFGSSVPEKQSRCVNIEWHRFRFGQDQ
          LLHGSKNVTNSSCLKLARQNSNG.QKNKPREH.IDCGDIVWSLAFGSSVPEKQSRCVN.EWHRF.FGQDQ
Retrocopy LLHGSKNVTNSSCLKLARQNSNGAQKNKPREHVIDCGDIVWSLAFGSSVPEKQSRCVNREWHRF*FGQDQ

Parental  LLLATGLNNGRIKIWDVYTGKLLLNLVDHIEVVRDLTFAPDGSLLLVSASRDKTLRVWDLKDDGNMVKVL
          LLLATGLNNGRIKIWDVYTGKL.L.L.DHIEVVRDLTFAP.GSLLL.SASRD..LRVWDLK.DGNM....
Retrocopy LLLATGLNNGRIKIWDVYTGKLFLDLADHIEVVRDLTFAPGGSLLLLSASRDNILRVWDLKGDGNM-SIV

Parental  RGHQNWVYSCAFS
          ......V..C.FS
Retrocopy GPSELGVQLCVFS

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	93.03 RPM
SRP017611_kidney	0.00 RPM	86.67 RPM
SRP017611_liver	0.00 RPM	43.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2136 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2136 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000012929	1 retrocopy	retro_rnor_2136 ,
Rattus norvegicus	ENSRNOG00000018027	1 retrocopy	retro_rnor_509,