RetrogeneDB ID: retro_mmus_487

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:131632508..131632969(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000095841
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ap1s3
• Ensembl ID: ENSMUSG00000054702
• Aliases: Ap1s3, 1190009B22, Jr2, [s]3A
• Description: adaptor-related protein complex AP-1, sigma 3 [Source:MGI Symbol;Acc:MGI:1891304]

Sequence

>retro_mmus_487
ATGATACATTTCATCTTGCTCTTCAGTCGACAAGGGAAGCTGCAGCTGCAGAAATGGTACACCACACTTCCTGACAAGGA
GAGGAAGAAATCACCCGAGACATCATCCAGACGGTCCTCTCTCGTGGGCGCAGGACCAGCAGCTTCATTGACTGGAAGGA
GCTGAAACTTGTTTATAAAAGGTACGCTAGTTTATATTTTTGCTGTGCAATAGAAAATCAAGACAATGAGCTATTGACAC
TAGAGATTGTTCATCGTTATGTGGAGTTGCTGGATAAATACTTTGGAAATGTCTGTGAGCTGGATATTATCTTTAATTTT
GAAAAGGCATATTTTATCCTTGATGAGTTTATAATAGGTGGAGAAATTCAGGAAACATCCAAGAAAACAGCAGTCAAGGC
CATTGAAGACTCTGATATGTTACAAGAGACAATGGAAGAATACATGAACAAGCCCGCGTTT

Alignment

ORF - retro_mmus_487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.42 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIHFILLFSRQGKLRLQKWYTTLPDKERKK-ITRDIIQTVLSRGHRTSSFIDWKELKLVYKRYASLYFCC
          MIHFILLFSRQGKL.LQKWYTTLPDKERKK.ITRDIIQTVLSRG.RTSSFIDWKELKLVYKRYASLYFCC
Retrocopy MIHFILLFSRQGKLQLQKWYTTLPDKERKK<ITRDIIQTVLSRGRRTSSFIDWKELKLVYKRYASLYFCC

Parental  AIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIGGEIQETSKKTAVKAIEDSD
          AIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIGGEIQETSKKTAVKAIEDSD
Retrocopy AIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIGGEIQETSKKTAVKAIEDSD

Parental  MLQETMEEYMNKPTF
          MLQETMEEYMNKP.F
Retrocopy MLQETMEEYMNKPAF

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	1.75 RPM
SRP007412_cerebellum	0.00 RPM	0.87 RPM
SRP007412_heart	0.00 RPM	0.34 RPM
SRP007412_kidney	0.00 RPM	6.43 RPM
SRP007412_liver	0.00 RPM	0.71 RPM
SRP007412_testis	0.00 RPM	0.23 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_487 was not detected

EST

No EST(s) were mapped for retro_mmus_487 retrocopy.

TSS

No TSS is located nearby retro_mmus_487 retrocopy 5' end.

Lab

retro_mmus_487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_487 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011939	5 retrocopies	retro_chof_113, retro_chof_1230, retro_chof_1299, retro_chof_1949, retro_chof_2099,
Callithrix jacchus	ENSCJAG00000012352	2 retrocopies	retro_cjac_3187, retro_cjac_3903,
Macropus eugenii	ENSMEUG00000016580	11 retrocopies	retro_meug_1074, retro_meug_1342, retro_meug_1488, retro_meug_168, retro_meug_1864, retro_meug_289, retro_meug_318, retro_meug_361, retro_meug_816, retro_meug_909, retro_meug_938,
Microcebus murinus	ENSMICG00000014406	1 retrocopy	retro_mmur_1492,
Monodelphis domestica	ENSMODG00000021198	1 retrocopy	retro_mdom_1427,
Mus musculus	ENSMUSG00000008036	1 retrocopy	retro_mmus_2739,
Mus musculus	ENSMUSG00000054702	3 retrocopies	retro_mmus_2202, retro_mmus_2799, retro_mmus_487 ,
Ochotona princeps	ENSOPRG00000013358	1 retrocopy	retro_opri_443,
Pan troglodytes	ENSPTRG00000012979	1 retrocopy	retro_ptro_2258,
Sarcophilus harrisii	ENSSHAG00000010973	1 retrocopy	retro_shar_695,