RetrogeneDB ID: retro_rnor_1783

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:26787802..26788187(+)
• 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_1783
GGGCAGCGCCACGCCATGGTTGCTTGTTACCCAGGCAACAAAATAGGCTATGTCCATCACATCAATAACCCAAATGGAGA
AGGAAGACTCAGGACCTGTATGCATTATCTAAATAAAAACTGGGACGCCAAGGTAAGTGGAGGTATCATTCGAATTTTTC
CAGGAAGGCAAAGCCCAGTTTGCTGTCAGTGAACCCAAATTTGATCCACTGCTGTTTTTCTGGTCTGACAGGCATAACGC
TCATCAGGTACAGACAGCACACACTACCAGGTATCCAATAACTGTTTGCTATTTTGAGGCAGATGAGCGAGCAAAAGCTA
AAGTAAAATATCTAATCGGCGAGAAAAGTGTGAGCATTGAAATGAAGCCCCAATCAGTCAGCAAA

Alignment

ORF - retro_rnor_1783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.87 %
• Parental protein coverage: 57.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFP-EGKAQFADIEPKFDR
          G...AMVACYPGN..GYV.H..NPNG.GR..TC..YLNK.WDAKVSGGI.RIFP.EGKAQFA..EPKFD.
Retrocopy GQRHAMVACYPGNKIGYVHHINNPNGEGRLRTCMHYLNKNWDAKVSGGIIRIFP>EGKAQFAVSEPKFDP

Parental  LLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGEKGVRVELKPNSVSK
          LLFFWSDR.N.H.VQ.A..TRY.ITV.YF.ADERA.AKVKYL.GEK.V..E.KP.SVSK
Retrocopy LLFFWSDRHNAHQVQTAHTTRYPITVCYFEADERAKAKVKYLIGEKSVSIEMKPQSVSK

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_1783 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1783 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1783 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,