RetrogeneDB ID: retro_rnor_576

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:41830097..41830523(-)
• Located in intron of: ENSRNOG00000016011

Retrocopy information

• Ensembl ID: ENSRNOG00000021744
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BRMS1
• Ensembl ID: ENSRNOG00000047683
• Aliases: None
• Description: None

Sequence

>retro_rnor_576
ATGCCCATCCAGGCTTCAGGCAAAGAAACAGAAGAGATGGAGGCAGAAGGCGATTCAGCAGCTGAGATGAGTGGGGAGGC
AGATGAGAGTGAGGAGGAATGGAGAGGCAGCCAGACTGAGTCAGAGGAGGAGAGCTCAGAGATGGATGACGAGGACAGTG
AGTGTGTCAGTGAGATGCTGGACCCGGAAAAGCAGTTCTTGGAGCTGAAGAAGTTGTTCAGAGAATGGCTGAGCGAGCTG
CGATTACAACTGGAGGAAGTGGGGGCCGAGAGAGCCCCAGAATATACAGAGCCTCTTGGAGGGCTGCAGCAGAGCCTAAA
GGTTCGTATTCAGGTGGCAGGGATCTACAAGGGCTCCTGTCTGGATGTGATCAGGAGTAAGTATGAATGTGAACTACAGG
GAGCCGAACAGCACCTCGAGAGAGAG

Alignment

ORF - retro_rnor_576 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 60.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPIQPSGKETEEMEAEGDSAAEMNGEADESEEERSGSQTESEEESSEMDDEDYERRRSECVSEMLDLEKQ
          MPIQ.SGKETEEMEAEGDSAAEM.GEAD..E.E........E.E.......D.....SECVSEMLD.EKQ
Retrocopy MPIQASGKETEEMEAEGDSAAEMSGEAD--ESEEEWRGSQTESEEESSEMDDED---SECVSEMLDPEKQ

Parental  FSELKEKLFRERLSQLRLRLEEVGAERAPEYTEPLGGLQQSLKIRIQVAGIYKGFCLDVIRNKYECELQG
          F.ELK.KLFRE.LS.LRL.LEEVGAERAPEYTEPLGGLQQSLK.RIQVAGIYKG.CLDVIR.KYECELQG
Retrocopy FLELK-KLFREWLSELRLQLEEVGAERAPEYTEPLGGLQQSLKVRIQVAGIYKGSCLDVIRSKYECELQG

Parental  AKQHLESE
          A.QHLE.E
Retrocopy AEQHLERE

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_576 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_576 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012784	1 retrocopy	retro_cfam_2100,
Myotis lucifugus	ENSMLUG00000014596	1 retrocopy	retro_mluc_1168,
Rattus norvegicus	ENSRNOG00000047683	1 retrocopy	retro_rnor_576 ,