RetrogeneDB ID: retro_mmus_3022

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:41682856..41683300(-)
• Located in intron of: ENSMUSG00000074164

Retrocopy information

• Ensembl ID: ENSMUSG00000092193
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cd9
• Ensembl ID: ENSMUSG00000030342
• Aliases: Cd9, Tspan29
• Description: CD9 antigen [Source:MGI Symbol;Acc:MGI:88348]

Sequence

>retro_mmus_3022
TCAAAGTGCATCAAATACCTGTTCTTCAGATTTAACTTCATCTTCTGGCTCGCTGGCATTGAAGTGCTTGCTATTGGACT
ATGGCTCTGATTTGACTCTCAGACCAAGAGCATCTTCGAGCAAGAGACTAACCATTTCAGTTTCTGCACAGGAGTGTACA
TTCTGATTGGAGCCGGGGCCCTCATGATGCTGGTTGGTTTCCTGGGCTGGTGTGGAGCTGTACAAGAGTCCCAGTGCATG
CTGGGGTTGTTCTTCGGGTTCCTCTTGGTGGTATTTGCCATTGAGATAGCTGCCACAGTCTGGGGCTATACCCACAAGGA
TGAGGTGATTAAAGAAGTCCTGGAGTTTTACAACGACACCTACCAAAAGTTACGGAGCAAGGATGAACCCACGCGGGAAA
CACTCAAAGCCATTCATATGGCTTGGAACTGCTGTGGCATAGCA

Alignment

ORF - retro_mmus_3022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.19 %
• Parental protein coverage: 65.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKCIKYLLFGFNFIFWLAGIAVLAIGLWLRFDSQTKSIFEQENNHSSFYTGVYILIGAGALMMLVGFLGC
          SKCIKYL.F.FNFIFWLAGI.VLAIGLWL.FDSQTKSIFEQE.NH.SF.TGVYILIGAGALMMLVGFLG.
Retrocopy SKCIKYLFFRFNFIFWLAGIEVLAIGLWL*FDSQTKSIFEQETNHFSFCTGVYILIGAGALMMLVGFLGW

Parental  CGAVQESQCMLGLFFGFLLVIFAIEIAAAVWGYTHKDEVIKELQEFYKDTYQKLRSKDEPQRETLKAIHM
          CGAVQESQCMLGLFFGFLLV.FAIEIAA.VWGYTHKDEVIKE..EFY.DTYQKLRSKDEP.RETLKAIHM
Retrocopy CGAVQESQCMLGLFFGFLLVVFAIEIAATVWGYTHKDEVIKEVLEFYNDTYQKLRSKDEPTRETLKAIHM

Parental  ALDCCGIA
          A..CCGIA
Retrocopy AWNCCGIA

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	19.30 RPM
SRP007412_cerebellum	0.00 RPM	15.68 RPM
SRP007412_heart	0.00 RPM	20.55 RPM
SRP007412_kidney	0.00 RPM	26.91 RPM
SRP007412_liver	0.00 RPM	7.95 RPM
SRP007412_testis	0.14 RPM	2.65 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3022 was not detected

EST

No EST(s) were mapped for retro_mmus_3022 retrocopy.

TSS

No TSS is located nearby retro_mmus_3022 retrocopy 5' end.

Lab

retro_mmus_3022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3022 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009313	1 retrocopy	retro_eeur_174,
Felis catus	ENSFCAG00000006863	1 retrocopy	retro_fcat_1098,
Myotis lucifugus	ENSMLUG00000006901	1 retrocopy	retro_mluc_2384,
Monodelphis domestica	ENSMODG00000018053	3 retrocopies	retro_mdom_1490, retro_mdom_226, retro_mdom_872,
Mus musculus	ENSMUSG00000030342	1 retrocopy	retro_mmus_3022 ,
Ictidomys tridecemlineatus	ENSSTOG00000001348	1 retrocopy	retro_itri_768,