RetrogeneDB ID: retro_rnor_1205

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:86151665..86152098(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Susd3
• Ensembl ID: ENSRNOG00000016525
• Aliases: None
• Description: sushi domain-containing protein 3 [Source:RefSeq peptide;Acc:NP_001100811]

Sequence

>retro_rnor_1205
GCCGGGAACACAACACAGGTCCCGGGGAAACAGACAGGTACCTGTGCTCAGCTCTATCCCCCACCCACCTGCCCCCCTCA
AGGCACCTTGCAAGTTGTCCGTGGAGATGGCCCTTCACTGCGGACTGTGCTCATATTTCACTGCCCCACTGGCCCCCAGA
TGGTGGGGTCTGTCTGGCATCCTTACTTGTTCCTGGAACGGGAGCGCCGTTGACTGGTCTTCGGGAAACCCCGTGTGCGA
AGCTGTGCCGCTGTATGAGACCTTACGCTTCAGTGTGACAGTAATTGCCTCCATCGTGAGCTGTGCCATCCCTCTGCTCA
TGTCCATGGCCTTCCTCACCTGCTGCCTCCTCAAGTGCGTACAGAGGAGTGAGAAGCGGCGTGCTGACAGGATGACACAG
CTGTGGTACCAGCTGAGAGGTGAGGACCTAGAG

Alignment

ORF - retro_rnor_1205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.97 %
• Parental protein coverage: 51.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGNTTPPVPGNQTGTCAQLHP----PPKGTLQVVRGDGTSLGTVLI-FHCPSGHQMVG-SGLLTCAWNGS
          AGNTT..VPG.QTGTCAQL.P....PP.GTLQVVRGDG.SL.TVLI.F..P......G.SG.LTC.WNGS
Retrocopy AGNTTQ-VPGKQTGTCAQLYPPPTCPPQGTLQVVRGDGPSLRTVLI>FTAPLAPRWWGLSGILTCSWNGS

Parental  TADWSSGSPVCKAVPPHETFGFKVAVIASIVSCAIILLMSMAFLTCCLLKCVQKSEQRRADRTAQLWYQL
          ..DWSSG.PVC.AVP..ET..F.V.VIASIVSCAI.LLMSMAFLTCCLLKCVQ.SE.RRADR..QLWYQL
Retrocopy AVDWSSGNPVCEAVPLYETLRFSVTVIASIVSCAIPLLMSMAFLTCCLLKCVQRSEKRRADRMTQLWYQL

Parental  RGEDLE
          RGEDLE
Retrocopy RGEDLE

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	1.80 RPM
SRP017611_kidney	0.00 RPM	24.42 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_1205 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1205 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1205 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001297	1 retrocopy	retro_acar_95,
Ochotona princeps	ENSOPRG00000005344	2 retrocopies	retro_opri_234, retro_opri_581,
Rattus norvegicus	ENSRNOG00000016525	1 retrocopy	retro_rnor_1205 ,