RetrogeneDB ID: retro_rnor_2109

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:228961208..228961597(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Egln1
• Ensembl ID: ENSRNOG00000019773
• Aliases: None
• Description: Egl nine homolog 1 [Source:UniProtKB/Swiss-Prot;Acc:P59722]

Sequence

>retro_rnor_2109
GGACAACAATAGGCCATGGTTGCTTGTTACCCAGTCAACAGAACATGCTCTAACCATCACGTCAGTAACTCAAATGCAGA
TAGAAGATGCATGACTTGTATGTATTATCTATTTAAATACTGGGACGCCAAGGTAAGTGGAGGTACTCTTCGATTTTTTT
CTAGAAGTCAATGCCTACTTTGCTGGCATTGAACCTAATTTGATAAACTGCTGTTTTTCTTGTGTGATAGGCATAACCCT
CATCAAATACAGTGTGCATACACTACAAGGTGTTTAATTACTCTTTGATATTTTGATGCAGATGAACAAGTGAAGCTAAA
GTAAAATATCTAATAGGCTAGAATGGTGTGAGCTTTGAACTCAAGCAACAATCAGTCAGCAAAAATGTC

Alignment

ORF - retro_rnor_2109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.65 %
• Parental protein coverage: 58.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFP-EGKAQFADIEPK-FD
          G...AMVACYP.N.T....HV.N.N.D.RC.TC.YYL.K.WDAKVSGG.LR.F..E..A.FA.IEP..FD
Retrocopy GQQ*AMVACYPVNRTCSNHHVSNSNADRRCMTCMYYLFKYWDAKVSGGTLRFFS>EVNAYFAGIEPN<FD

Parental  RLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERAR-AKVKYLTGEKGVRVELKPNSVSKDV
          .LLFF..DR.NPH..Q.AY.TR..IT..YFDADE....AKVKYL.G..GV..ELK..SVSK.V
Retrocopy KLLFFLCDRHNPHQIQCAYTTRCLITL*YFDADEQVK<AKVKYLIG*NGVSFELKQQSVSKNV

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	19.20 RPM
SRP017611_kidney	0.00 RPM	28.05 RPM
SRP017611_liver	0.00 RPM	6.72 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2109 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2109 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007202	1 retrocopy	retro_etel_1722,
Rattus norvegicus	ENSRNOG00000019773	11 retrocopies	retro_rnor_1086, retro_rnor_1783, retro_rnor_2109 , retro_rnor_2110, retro_rnor_2411, retro_rnor_2885, retro_rnor_2938, retro_rnor_2939, retro_rnor_2955, retro_rnor_507, retro_rnor_948,
Ictidomys tridecemlineatus	ENSSTOG00000023570	1 retrocopy	retro_itri_1697,