RetrogeneDB ID: retro_rnor_1506

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:88437569..88437855(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Crb3
• Ensembl ID: ENSRNOG00000047322
• Aliases: None
• Description: crumbs protein homolog 3 precursor [Source:RefSeq peptide;Acc:NP_001020832]

Sequence

>retro_rnor_1506
ACTCCAGGCCGGGGGCTGCTCTTGGTATTTGACTTGCTGATTCTGCCCTCTGCCTGGAGCCTACCAACACTGGAGCCTTT
CACAAATCGCACACCTCAACCCCCAGGAGACAGGTCCAATGCGGGTCTGTCTTCAGAGGCTATTGTAGCCATCACAATGG
TCTTTTCCACTCTGGGAGTCCTTCTCATAGCAGTGGAGCTGTTCCTGCTAAGGTGAAAAGTTCTAGAAAGCTGCAAAGAG
AGGGCACCTAGGGCCCAGCAGCGAGGAGCAGTTTTCCTACAAAGCT

Alignment

ORF - retro_rnor_1506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.65 %
• Parental protein coverage: 85.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TPGLGLLLAFGLPMLPSGWSQETPDSFTNSTTQPPDGGGSNGGLSSEAIVAITVVFSILGTLLIAVGLFL
          TPG.GLLL.F.L..LPS.WS..T...FTN.T.QPP.G..SN.GLSSEAIVAIT.VFS.LG.LLIAV.LFL
Retrocopy TPGRGLLLVFDLLILPSAWSLPTLEPFTNRTPQPP-GDRSNAGLSSEAIVAITMVFSTLGVLLIAVELFL

Parental  LMRKLRE-KRQTEGT-YRPSSEEQVGARA
          L..K..E.K.Q.EGT...PSSEEQ....A
Retrocopy LR*KVLE<KLQREGT<LGPSSEEQFSYKA

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	0.29 RPM
SRP017611_kidney	0.00 RPM	24.14 RPM
SRP017611_liver	0.00 RPM	10.69 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1506 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1506 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016567	1 retrocopy	retro_cjac_868,
Homo sapiens	ENSG00000130545	2 retrocopies	retro_hsap_2747, retro_hsap_3478,
Gorilla gorilla	ENSGGOG00000007070	2 retrocopies	retro_ggor_1910, retro_ggor_2345,
Macaca mulatta	ENSMMUG00000005599	1 retrocopy	retro_mmul_1434,
Nomascus leucogenys	ENSNLEG00000015936	1 retrocopy	retro_nleu_1543,
Pongo abelii	ENSPPYG00000009457	2 retrocopies	retro_pabe_2222, retro_pabe_2873,
Pan troglodytes	ENSPTRG00000010367	1 retrocopy	retro_ptro_2984,
Rattus norvegicus	ENSRNOG00000047322	1 retrocopy	retro_rnor_1506 ,
Ictidomys tridecemlineatus	ENSSTOG00000002396	1 retrocopy	retro_itri_781,