RetrogeneDB ID: retro_mmus_3320

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:21608038..21608321(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arl14epl
• Ensembl ID: ENSMUSG00000073568
• Aliases: Arl14epl, Gm949
• Description: ADP-ribosylation factor-like 14 effector protein-like [Source:MGI Symbol;Acc:MGI:2685795]

Sequence

>retro_mmus_3320
GAACCATCACAGAAGAACAACTCCACTCAAGAGGGGCGCACTAACCACAGGTTTCCAGAGAAAAGCAGTCAGATTGGACA
GAAGCAACTGCAACAGATAGGACGGCGGCAGCTAAAGTGCTTAGCATTTCAAAACCCTGGACCTCAGGTGGCAGACTTCA
ACTGAGACAAGGCAGCAGAGAAGGAAAGCGCGGATGTCAAAGAAGGTGAATGAATACTTTTCTGTGAAGTACAAGGTGAT
GAAGAAGTACGGCAAAAGCGGCAGGCTGATCTGTGACGACGTG

Alignment

ORF - retro_mmus_3320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 61.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPSQKNNSTQQELTNHLFPEKSSQIGQKQLQQI-ERQLKCLAFQNPGPQVADFN-PETRQQKKKARMSKM
          EPSQKNNSTQ...TNH.FPEKSSQIGQKQLQQI..RQLKCLAFQNPGPQVADFN.....Q..K.....K.
Retrocopy EPSQKNNSTQEGRTNHRFPEKSSQIGQKQLQQIGRRQLKCLAFQNPGPQVADFN>ETRQQRRKARMSKKV

Parental  NEYFSVKYKVMKKYDKSGRLICNDV
          NEYFSVKYKVMKKY.KSGRLIC.DV
Retrocopy NEYFSVKYKVMKKYGKSGRLICDDV

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
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.03 RPM
SRP007412_kidney	0.04 RPM	0.00 RPM
SRP007412_liver	0.08 RPM	0.00 RPM
SRP007412_testis	0.46 RPM	22.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3320 was not detected

EST

No EST(s) were mapped for retro_mmus_3320 retrocopy.

TSS

No TSS is located nearby retro_mmus_3320 retrocopy 5' end.

Lab

retro_mmus_3320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3320 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000027122	1 retrocopy	retro_mmus_3319,
Mus musculus	ENSMUSG00000073568	1 retrocopy	retro_mmus_3320 ,
Rattus norvegicus	ENSRNOG00000025590	3 retrocopies	retro_rnor_1779, retro_rnor_2167, retro_rnor_514,