RetrogeneDB ID: retro_mmus_281

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:24493206..24493656(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000057160
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Arpc5
• Ensembl ID: ENSMUSG00000008475
• Aliases: Arpc5, 5830443F10Rik, p16-Arc
• Description: actin related protein 2/3 complex, subunit 5 [Source:MGI Symbol;Acc:MGI:1915021]

Sequence

>retro_mmus_281
ATGCCGAAGAACACGGTGTCGTCGGCCCGCTTCCGGAAGGTGGACGTGGACGAATATGAGGAGAACAAGTTCGTGGACGA
GGAGGACGGCGGCGATGGCCAGGCCGGGCCCGACGAGGGCGAGGTGGACTCGTGCCTACCGCAAGGAAACATGACAGCTG
CTCTGAAATCCCCCCCACCCCCCACTATTAACACAAAGAGCCAGGCAGTGAAGGACTGTGCTGGCAGCTACGTCTTGAAG
GTGCTTATCTCTTTTAAAGCTAATGATATTGAAAAGGCAGTTCAGTCTCTGGACAAGAACGGTGTGGACCTCCTAATGAA
GTGTATTTATAAAGGCTCTGAGAGCCCATCTGACAACAGCAGTGCTGTGTTGCTGCAGTGGCATGAAAAGGCACTTGCTG
AGGGAGGAGTGGGGTCCATCGTTCGCGTTTTGACTGCAAGGAAAACCGTG

Alignment

ORF - retro_mmus_281 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALKNPPINTKSQA
          M.KNTVSSARFRKVDVDEY.ENKFVDEEDGGDGQAGPDEGEVDSCL.QGNMTAAL......P.INTKSQA
Retrocopy MPKNTVSSARFRKVDVDEYEENKFVDEEDGGDGQAGPDEGEVDSCLPQGNMTAALKSP-PPPTINTKSQA

Parental  VKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDNSSAVLLQWHEKALAAGGVGS
          VKD.AGS.VLKVLISFKANDIEKAVQSLDKNGVDLLMK.IYKG.ESPSDNSSAVLLQWHEKALA.GGVGS
Retrocopy VKDCAGSYVLKVLISFKANDIEKAVQSLDKNGVDLLMKCIYKGSESPSDNSSAVLLQWHEKALAEGGVGS

Parental  IVRVLTARKTV
          IVRVLTARKTV
Retrocopy IVRVLTARKTV

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	0.02 RPM	55.86 RPM
SRP007412_cerebellum	0.00 RPM	23.66 RPM
SRP007412_heart	0.03 RPM	21.20 RPM
SRP007412_kidney	0.04 RPM	46.66 RPM
SRP007412_liver	0.05 RPM	46.07 RPM
SRP007412_testis	0.14 RPM	16.19 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_281 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	12:24493056..24493902
ENCFF001YKA	POLR2A	12:24493337..24493847

EST

No EST(s) were mapped for retro_mmus_281 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_22430	379 libraries	453 libraries	201 libraries	39 libraries	0 libraries

The graphical summary, for retro_mmus_281 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_281 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000560	2 retrocopies	retro_chof_1502, retro_chof_783,
Dasypus novemcinctus	ENSDNOG00000010375	3 retrocopies	retro_dnov_1277, retro_dnov_199, retro_dnov_2495,
Equus caballus	ENSECAG00000019128	1 retrocopy	retro_ecab_1104,
Echinops telfairi	ENSETEG00000014969	1 retrocopy	retro_etel_1922,
Monodelphis domestica	ENSMODG00000007194	1 retrocopy	retro_mdom_968,
Mus musculus	ENSMUSG00000008475	1 retrocopy	retro_mmus_281 ,
Rattus norvegicus	ENSRNOG00000028062	1 retrocopy	retro_rnor_1873,
Tupaia belangeri	ENSTBEG00000006295	8 retrocopies	retro_tbel_1822, retro_tbel_1933, retro_tbel_1962, retro_tbel_2504, retro_tbel_3191, retro_tbel_3192, retro_tbel_3197, retro_tbel_3806,