RetrogeneDB ID: retro_rnor_1908

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:111743055..111743724(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Twf2
• Ensembl ID: ENSRNOG00000048915
• Aliases: None
• Description: twinfilin, actin-binding protein, homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:1346078]

Sequence

>retro_rnor_1908
GGCCACATCAAGGATGAGCTCTCCTTGGCTGGGTACCAGAAGCACCTGTCATCTTGTGCTGCACCTGCCCCACTGACTTC
AGCTGAGCGAGAGCTCCAGCAGATCCAAATCAATGAGGTGAAGACTGAGATCAGCGTGGAAAGCAAGCACCAGACCCTGC
AGGGCCTGGCCTTCCCCCTGCTGCCTGAGGCCCAGCGGGCACTTCAGCAACTCCAGCAGAAGACAGTCAACTATATCCAG
CTGAAGCTGGACCTGTAACGGGAGACCATCGAGCTGGTACACACAGAACCCACAAATGTGGCCCAGCTGCCCTCACGGGT
ACCCAGAGATGCTGCCCATTACCACTTCTTCCTGTACAAGCATACCCATGAGGGTGACTCCCTTGAATCTGTGGTGTTCA
TCTTCTCCAAGCCGGGGTACAAGTGCAGCATTAAGGAGCGCATGCTCTATTCCAGCTGCGAAAGCTGCCTCCTTGACTCT
GTAGAGCAAGACTTCCAGCTGGAGATCGCTAAGAAGATTGAGATCGGCGATGGGGCGGAGCTGACCGCTGAGTTCCTCTA
TGATGAAGTGCATCCCAAGCAGCACGCCTTCAAGCAGGCATTCTCCAAGCCCAAAGACCCTGGAGGCAAGCAGGGCCACA
AGCGCCTTATCCGCGGCCCCGGGGAGAAT

Alignment

ORF - retro_rnor_1908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.27 %
• Parental protein coverage: 63.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTVKDDLSLAGYQKHLSSCAAPAPLTSAERELQQIRINEVKTEISVESKHQTLQGLAFPLQPEAQRALQQ
          G..KD.LSLAGYQKHLSSCAAPAPLTSAERELQQI.INEVKTEISVESKHQTLQGLAFPL.PEAQRALQQ
Retrocopy GHIKDELSLAGYQKHLSSCAAPAPLTSAERELQQIQINEVKTEISVESKHQTLQGLAFPLLPEAQRALQQ

Parental  LKQKTVNYIQLKLDLERETIELVHTEPTNVAQLPSRVPRDAARYHFFLYKHTHEGDSLESVVFIYSMPGY
          L.QKTVNYIQLKLDL.RETIELVHTEPTNVAQLPSRVPRDAA.YHFFLYKHTHEGDSLESVVFI.S.PGY
Retrocopy LQQKTVNYIQLKLDL*RETIELVHTEPTNVAQLPSRVPRDAAHYHFFLYKHTHEGDSLESVVFIFSKPGY

Parental  KCSIKERMLYSSCKSRLLDSVEQDFQLEIAKKIEIGDGAELTAEFLYDEVHPKQHAFKQAFAKPKGPGGK
          KCSIKERMLYSSC.S.LLDSVEQDFQLEIAKKIEIGDGAELTAEFLYDEVHPKQHAFKQAF.KPK.PGGK
Retrocopy KCSIKERMLYSSCESCLLDSVEQDFQLEIAKKIEIGDGAELTAEFLYDEVHPKQHAFKQAFSKPKDPGGK

Parental  RGHKRLIRGPGEN
          .GHKRLIRGPGEN
Retrocopy QGHKRLIRGPGEN

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	0.14 RPM	23.87 RPM
SRP017611_kidney	0.14 RPM	4.61 RPM
SRP017611_liver	0.07 RPM	1.41 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1908 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1908 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1908 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000022507	1 retrocopy	retro_rnor_2176,
Rattus norvegicus	ENSRNOG00000048915	2 retrocopies	retro_rnor_1740, retro_rnor_1908 ,