RetrogeneDB ID: retro_rnor_1403

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:61469196..61469376(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lsm7
• Ensembl ID: ENSRNOG00000019552
• Aliases: None
• Description: U6 snRNA-associated Sm-like protein LSm7 [Source:RefSeq peptide;Acc:NP_001102202]

Sequence

>retro_rnor_1403
ATCTTGGACCTGTCTAAGTATATTGACAAGACCATCCACATGAAGTTCTAGGATGACTGGGAACCCAGAGGGATCCTGAG
AGAGTTTGACCCACTGAGCAACCTGGCACTGGACGGAACCACTGAGCTCGTGCAAGACCCCAATGACCAGTACAAGCTGA
TAGAGGGCACACAGCAGATG

Alignment

ORF - retro_rnor_1403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.0 %
• Parental protein coverage: 58.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPDDQYKLTEDTRQL
          ILDLSKYIDKTI..KF....E..GIL..FDPL.NL.LDGT.E...DP.DQYKL.E.T.Q.
Retrocopy ILDLSKYIDKTIHMKF*DDWEPRGILREFDPLSNLALDGTTELVQDPNDQYKLIEGTQQM

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	10.78 RPM
SRP017611_kidney	0.00 RPM	5.58 RPM
SRP017611_liver	0.00 RPM	4.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1403 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1403 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000013097	1 retrocopy	retro_mluc_331,
Mus musculus	ENSMUSG00000035215	1 retrocopy	retro_mmus_160,
Otolemur garnettii	ENSOGAG00000000144	3 retrocopies	retro_ogar_107, retro_ogar_2736, retro_ogar_2867,
Rattus norvegicus	ENSRNOG00000019552	1 retrocopy	retro_rnor_1403 ,