RetrogeneDB ID: retro_rnor_696

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:60569499..60569730(+)
• Located in intron of: ENSRNOG00000029537

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdc42se2
• Ensembl ID: ENSRNOG00000042449
• Aliases: Cdc42se2, RGD1563924
• Description: CDC42 small effector protein 2 [Source:UniProtKB/Swiss-Prot;Acc:A1L1K4]

Sequence

>retro_rnor_696
ATGAGTACATTCTGGTTGTGTTTGAACTGCTGTATTGCAGAGAAGCTTCAGTCTAAGAGGCAACAATAGGTTGACTGAAG
TATGGTGGAAGAGCTAACCAACTTTGTGCACATAGCTCACATAGGATCTGGAGACCTATTTAGTGGAACAAACTCAGTCA
GCTCCATTCAGAACCAAATGCAGTCCAAGAGAGGTTATGGAAGTGGAATGCCTGCTGATGTGCAGACACAA

Alignment

ORF - retro_rnor_696 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.03 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEFWLCFNCCIAEQPQPKRRRRIDRSMIGEPTNFVHTAHVGSGDLFSGMNSVSSIQNQMQSKGGYGGGM
          MS.FWLC.NCCIAE..Q.KR....D.SM..E.TNFVH.AH.GSGDLFSG.NSVSSIQNQMQSK.GYG.GM
Retrocopy MSTFWLCLNCCIAEKLQSKRQQ*VD*SMVEELTNFVHIAHIGSGDLFSGTNSVSSIQNQMQSKRGYGSGM

Parental  PANVQMQ
          PA.VQ.Q
Retrocopy PADVQTQ

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	91.45 RPM
SRP017611_kidney	0.00 RPM	38.31 RPM
SRP017611_liver	0.00 RPM	8.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_696 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_696 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_696 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
Choloepus hoffmanni	ENSCHOG00000008774	1 retrocopy	retro_chof_1622,
Cavia porcellus	ENSCPOG00000005142	1 retrocopy	retro_cpor_367,
Rattus norvegicus	ENSRNOG00000042449	2 retrocopies	retro_rnor_461, retro_rnor_696 ,