RetrogeneDB ID: retro_rnor_1779

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:22216701..22217103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arl14epl
• Ensembl ID: ENSRNOG00000025590
• Aliases: None
• Description: Protein LOC685394 [Source:UniProtKB/TrEMBL;Acc:D3ZBL0]

Sequence

>retro_rnor_1779
GTTTATCCTGTTAGGTTGGCAAGGCTGGCTGGTGACCAGCAGCAACTGATCGAACGGCAGCTAAAGTGATTAACAGTTCA
GAACCATAGACTTCACGTGGCAGATTTTAACCTTGAGACAAGGCAGCCTGAAAAGAAAGCACTGATGTTGAAGATGAGTG
GATATTTTTCTGTGAAGTACAAGGCGATGAATAAGTACGACAAAAACAGCAGGCTGCTGTGTAACGATGTGGACCTGTGT
GACAGTCTAGAGAAGAACTGCCTGGGATGCTTCTACCCAGGTCCCAAGTGCAACTCCAACAAGTATGGGCCAGAGCGCCA
GTGGAACTTGTGCTGGGTCAATGATGCCATCATCATAGAGTCTGGTGAGGTCATCAGCACCCTGCCATTTTTTGTTCCTG
AT

Alignment

ORF - retro_rnor_1779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.66 %
• Parental protein coverage: 88.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFPEKSSQIGQKQLQQIERQLKCLAFQNPGPQVADFNPETRQQKKKARMSKMNEYFSVKYKVMKKYDKNG
          V.P.........Q.Q.IERQLK.L..QN....VADFN.ETRQ..KKA.M.KM..YFSVKYK.M.KYDKN.
Retrocopy VYPVRLARLAGDQQQLIERQLK*LTVQNHRLHVADFNLETRQPEKKALMLKMSGYFSVKYKAMNKYDKNS

Parental  RLICNDVDLCDCLEKNCLGCFYPCPKCNSNKCGPECRCNRRWVYDAIVTESGEVISTLPFSVPD
          RL.CNDVDLCD.LEKNCLGCFYP.PKCNSNK.GPE...N..WV.DAI..ESGEVISTLPF.VPD
Retrocopy RLLCNDVDLCDSLEKNCLGCFYPGPKCNSNKYGPERQWNLCWVNDAIIIESGEVISTLPFFVPD

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1779 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1779 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1779 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000073568	1 retrocopy	retro_mmus_3320,
Rattus norvegicus	ENSRNOG00000025590	3 retrocopies	retro_rnor_1779 , retro_rnor_2167, retro_rnor_514,