RetrogeneDB ID: retro_rnor_2833

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:86282495..86282965(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ivns1abp
• Ensembl ID: ENSRNOG00000002618
• Aliases: None
• Description: influenza virus NS1A binding protein [Source:RefSeq peptide;Acc:NP_001040550]

Sequence

>retro_rnor_2833
GAGGAATGTTTGTGAACAGTTGAATGCTATGATCCACATTCAAATCATTGGTCCTTCCTCCCTCCCATGAGAACACCAAG
TGACCACTTTCCAATGGCTGTACTGATGGGACAGAGCTCTATGTGGTAGGTGGGTCAAATGGAAACTCAGATGACCTGAA
TTGTGGAGAAATGTATGATTCAAGCATTGATGACTGCACCCCTATTTCAGAGTTGAGAACTAACCATATTAATGCAGAAG
TGTGTATTCTGAATGGGAAATTGTACATTGTTGGTTGCTTTGAAGCATATGGTCAGAAAGAACTGAAAAATTGTGATATA
TTTGATCCTGAAACAATGTCATGTACAAGCTGTACTCCTGTTAACATTCAAAGACACTAGTCTGCAGTTTGTGAACTTGG
TGGTTATTTGTACATAATTGGAGGTGCAGAATCTACACAGTAGAACAATGCAATCCTGAAAATGACACCT

Alignment

ORF - retro_rnor_2833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.09 %
• Parental protein coverage: 51.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EECLRTVECYDPHTDHWSFLAPMRTPRARFQMAVLMGQLYV-VGGSNGHSDD-LSCGEMYDPSIDDWTPV
          EECL.TVECYDPH..HWSFL.PMRTP...F.MAVLMGQ....V.G......D.L.CGEMYD.SIDD.TP.
Retrocopy EECL*TVECYDPHSNHWSFLPPMRTPSDHFPMAVLMGQSSM<VVGGSNGNSDDLNCGEMYDSSIDDCTPI

Parental  PELRTNRCNAGVCALNGKLYIVGGSDPYGQKGLKNCDVFDPVTKSWTSCAPLNIRRHQSAVCELGGYLYI
          .ELRTN..NA.VC.LNGKLYIVG....YGQK.LKNCD.FDP.T.S.TSC.P.NI.RH.SAVCELGGYLYI
Retrocopy SELRTNHINAEVCILNGKLYIVGCFEAYGQKELKNCDIFDPETMSCTSCTPVNIQRH*SAVCELGGYLYI

Parental  IGGAESWNCLNTVERYNP
          IGGAES....N......P
Retrocopy IGGAESTQ*NNAILKMTP

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	90.73 RPM
SRP017611_kidney	0.00 RPM	314.23 RPM
SRP017611_liver	0.00 RPM	63.54 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2833 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2833 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000002618	2 retrocopies	retro_rnor_2105, retro_rnor_2833 ,