RetrogeneDB ID: retro_rnor_2300

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:79668179..79668536(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pea15a
• Ensembl ID: ENSRNOG00000046996
• Aliases: Pea15, Pea15a
• Description: Astrocytic phosphoprotein PEA-15 [Source:UniProtKB/Swiss-Prot;Acc:Q5U318]

Sequence

>retro_rnor_2300
ATCACCACTACCATCACCCTTGAGTATCTGGAAGAGTTCAAGTCATCCTGCAAGGAGGACATTCCCAGCAAAAAGAGTGA
GAAAATTGCTGCAGGCAGTGCCTGGTTTCACTTCTCAGAGAGCCAAAACAAGCTAGACAAAGACAACACTTTATACTGAG
CACATCTTTCAGATATCTGTGCATGCTGACCTACTCAGATGGAGGTTGAGTACAGAGTCCATGTGCTGAAGATCTCCCAG
GAGGATGAGCTGCACACCAAGCTAACCAGTATCTTCAGAGCTAAGAAGTACAAAAAAAGTATGTGTCAGCCCTCTGAAGA
AGAAATCATCAAATTGGCTCCCCCATCAAAGAATTCC

Alignment

ORF - retro_rnor_2300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.39 %
• Parental protein coverage: 92.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTNNITLEDLEQLKSACKEDIPSEKSEEITTGSAWFSFLESHNKLD-KDNLSYIEHIFEISRRPDLLT-M
          .T..ITLE.LE..KS.CKEDIPS.KSE.I..GSAWF.F.ES.NKLD.K..L.Y.EHIF.IS...DLL..M
Retrocopy ITTTITLEYLEEFKSSCKEDIPSKKSEKIAAGSAWFHFSESQNKLD>KTTL-YTEHIFQISVHADLLR<M

Parental  VVDYRTRVLKISEEDELDTKLTRIPSAKKYKDIIRQPSEEEIIKLAPPPKKA
          .V.YR..VLKIS.EDEL.TKLT.I..AKKYK....QPSEEEIIKLAPP.K..
Retrocopy EVEYRVHVLKISQEDELHTKLTSIFRAKKYKKSMCQPSEEEIIKLAPPSKNS

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	361.42 RPM
SRP017611_kidney	0.00 RPM	55.83 RPM
SRP017611_liver	0.00 RPM	10.29 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2300 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2300 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_859

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000001275	1 retrocopy	retro_mluc_1340,
Mus musculus	ENSMUSG00000013698	1 retrocopy	retro_mmus_859,
Rattus norvegicus	ENSRNOG00000046996	1 retrocopy	retro_rnor_2300 ,