RetrogeneDB ID: retro_rnor_2788

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:37574291..37574774(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004319
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lamtor1
• Ensembl ID: ENSRNOG00000020016
• Aliases: Lamtor1, p18
• Description: Ragulator complex protein LAMTOR1 [Source:UniProtKB/Swiss-Prot;Acc:Q6P791]

Sequence

>retro_rnor_2788
ATGGGGTGCTGCTATAGCAGCGAAAACGAGGACTCGGACCAGGACCAGGAGGAGAGGAAGCTGTTGTTGGACCCCAGTAA
CACCCCTACCAAAGCCCTCAATGGAGCCGAGCCCAGCTACCATAGCCTGCCTTCAGCTCGCACAGATGAGCAGGCCCTGC
TTTCCTCCATCCTTGCCAAGACAGCTAGCAACATCATTGATGTGTCTGCCGCAGACTCCCAGGGCATGGAGCAGCATGAG
TACATGGACCGGGCAAGGCAGTACAGTACCCGCTTGGCTGTGCTTAGCAGCAGTCTGACCCATTGGAAGAAGCTGCCACC
GCTGCCATCTCTCACCAGCCAGCCCCACCAAGTGCTGGCCAGTGAGCCTATCCCTTTCTCTGACTTGCAGCAGGTCTCCA
GGATAGCTGCTTATGCCTATAGTGCACTTTCTCAGATCCGAGTGGATGCGAAAGAAGAGCTGGTTGTACAGTTTGGGATC
CCA

Alignment

ORF - retro_rnor_2788 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGCCYSSENEDSDQDQEERKLLLDPSNTPTKALNGAEPSYHSLPSARTDEQALLSSILAKTASNIIDVSA
          MGCCYSSENEDSDQDQEERKLLLDPSNTPTKALNGAEPSYHSLPSARTDEQALLSSILAKTASNIIDVSA
Retrocopy MGCCYSSENEDSDQDQEERKLLLDPSNTPTKALNGAEPSYHSLPSARTDEQALLSSILAKTASNIIDVSA

Parental  ADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAY
          ADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAY
Retrocopy ADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAY

Parental  SALSQIRVDAKEELVVQFGIP
          SALSQIRVDAKEELVVQFGIP
Retrocopy SALSQIRVDAKEELVVQFGIP

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	0.07 RPM	17.18 RPM
SRP017611_kidney	0.21 RPM	30.84 RPM
SRP017611_liver	0.00 RPM	12.10 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_2788 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DW389228	37574290	37574534	99.6	243	1	242

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2788 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010854	2 retrocopies	retro_amel_1176, retro_amel_436,
Macropus eugenii	ENSMEUG00000003560	1 retrocopy	retro_meug_17,
Mus musculus	ENSMUSG00000030842	2 retrocopies	retro_mmus_1805, retro_mmus_2538,
Rattus norvegicus	ENSRNOG00000020016	1 retrocopy	retro_rnor_2788 ,
Tarsius syrichta	ENSTSYG00000014730	2 retrocopies	retro_tsyr_1324, retro_tsyr_33,