RetrogeneDB ID: retro_rnor_2661

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:5090371..5091004(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Taldo1
• Ensembl ID: ENSRNOG00000018367
• Aliases: None
• Description: Transaldolase [Source:UniProtKB/Swiss-Prot;Acc:Q9EQS0]

Sequence

>retro_rnor_2661
AAGTCCCAGGATGCCATCACCAACCCATCCATGACCCTGTCTGCAGCACAGATGCCTGCCTACCAAAAGCTGGTGCAGGA
AGCCACTACCTATAGCAAGAGGCTGGGTGGGACACAAGAGGAGCAGATTAAGCATGCCATTGATAAACGTTTTGTGTTGT
TTGGAGCAGAAATACTAAAAATTCCAGGCCATGTATCCACAGAAGTTGTTGCAAGGCTTTCCTTTGATAAAGATGCAATG
GTGGTCCAAGACAGGCACCTCACTGAGCTTTATGAAGAAGCTGGGATCAGCAAGGACAGAATTCTCATCATGTTATGATC
AACCTGGGAGGGAATCGAGGCTGGAACATTGTTGGAGGAGCAGCATGACATCCACTGGAATATGACACTGATTTTCTCCT
TCACCCAAGCTGTGCCCTGTACTGAAGCAGGTGTGACACTCATCTCTCCCTTTGTGGGCCACATCCTTGACTGGCATGTG
ACAAATACAGACAAGAAATCCTATCAACCCTAGAAGGACCCTGGAGTGAAGAGTATCACAAAAATCTACAACTACCACAA
AAATTTGGCCACAAGAGCATTGTCATGGGACCTCCTTCTGTAACATGAGTGAGATCAGGCTGTCACAGGCTGT

Alignment

ORF - retro_rnor_2661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 63.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KPQDATTNPSLILAAAQMPAYQELVEEAIAYGKKLGGPQEEQIKNAIDKLFVLFGAEILKKIPGRVSTEV
          K.QDA.TNPS..L.AAQMPAYQ.LV.EA..Y.K.LGG.QEEQIK.AIDK.FVLFGAEILK.IPG.VSTEV
Retrocopy KSQDAITNPSMTLSAAQMPAYQKLVQEATTYSKRLGGTQEEQIKHAIDKRFVLFGAEILK-IPGHVSTEV

Parental  DARLSFDKDAMVARARRIIELYKEAGISKDRILIKLSSTWEGIQAGKELEEQHGIHCNMTLLFSFAQAVA
          .ARLSFDKDAMV...R...ELY.EAGISKDRILI.L.STWEGI.AG..LEEQH.IH.NMTL.FSF.QAV.
Retrocopy VARLSFDKDAMVVQDRHLTELYEEAGISKDRILIML*STWEGIEAGTLLEEQHDIHWNMTLIFSFTQAVP

Parental  CAEAGVTLISPFVGRILDWHVANTDKKSYEPQEDPGVKSVTKIYNYYK-KFGYKTIVM-GASFRNTGEIK
          C.EAGVTLISPFVG.ILDWHV.NTDKKSY.P..DPGVKS.TKIYNY.K.KFG.K.IVM.G.SF.N..EI.
Retrocopy CTEAGVTLISPFVGHILDWHVTNTDKKSYQP*KDPGVKSITKIYNYHK<KFGHKSIVM<GTSFCNMSEIR

Parental  -ALAGC
          .A..GC
Retrocopy <AVTGC

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	50.54 RPM
SRP017611_kidney	0.00 RPM	166.71 RPM
SRP017611_liver	0.00 RPM	56.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2661 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2661 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2661 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010336	1 retrocopy	retro_btau_455,
Macropus eugenii	ENSMEUG00000000841	1 retrocopy	retro_meug_756,
Mus musculus	ENSMUSG00000025503	2 retrocopies	retro_mmus_645, retro_mmus_667,
Rattus norvegicus	ENSRNOG00000018367	1 retrocopy	retro_rnor_2661 ,
Xenopus tropicalis	ENSXETG00000001671	1 retrocopy	retro_xtro_16,