RetrogeneDB ID: retro_mmus_393

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:178143300..178143796(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tsnax
• Ensembl ID: ENSMUSG00000056820
• Aliases: Tsnax, R74833, Trax
• Description: translin-associated factor X [Source:MGI Symbol;Acc:MGI:1855672]

Sequence

>retro_mmus_393
ATGAACGGCAAAGAAGGACCAGGAGGGTTCAGGAAGATGAAACATAACGCCTTCCCACATAACCAAAGGAGAGAGGAGAA
GGATGCCAGTTTGTCTTCGCCGGTGATGCTGGCCTTCAAATCACTTCAGCAGGAGCTGGACACCAGGCACGACAAATATG
AGAGACTTGTGAAGCTAAGCCGGGATATTACTGTGGAAAGTAAGAGCACAATTTTTCTTCTCCATAGGATTACAAGTACT
CCTGATATGGAGGGAGATACTGACTGAATCAGAAAGTAAGCTGGATGGTGTCAGACAGAAGATCCTGCAGGTAGCCCAAG
ACCTGTCGGGGGAAGACATGCACCAGTTCCATTGAGCCGTCACCACAGGACTGCAGGAATATGTGGAGGCTGTCTCTTTT
CAACACTTCATCAAAACTCGTTCATTGATCAGTATGGAAGAGATTAACAAGCAGTTGGCATTTACAGCAGAAGACAGTGG
GAAAGAGAGCAAGACT

Alignment

ORF - retro_mmus_393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.77 %
• Parental protein coverage: 56.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNGKEGPGGFRKRKHDTFPHNQRREGKDASLSSPVMLAFKSFQQELDARHDKYERLVKLSRDITVESKRT
          MNGKEGPGGFRK.KH..FPHNQRRE.KDASLSSPVMLAFKS.QQELD.RHDKYERLVKLSRDITVESK.T
Retrocopy MNGKEGPGGFRKMKHNAFPHNQRREEKDASLSSPVMLAFKSLQQELDTRHDKYERLVKLSRDITVESKST

Parental  IFLLHRITSAPDME-EILTESESKLDGVRQKILQVAQELSGEDMHQFHRAVTTGLQEYVEAVSFQHFIKT
          IFLLHRITS.PDME.EILTESESKLDGVRQKILQVAQ.LSGEDMHQFH.AVTTGLQEYVEAVSFQHFIKT
Retrocopy IFLLHRITSTPDME>EILTESESKLDGVRQKILQVAQDLSGEDMHQFH*AVTTGLQEYVEAVSFQHFIKT

Parental  RSLISMEEINKQLTFTAEDSGKESKT
          RSLISMEEINKQL.FTAEDSGKESKT
Retrocopy RSLISMEEINKQLAFTAEDSGKESKT

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	0.40 RPM	151.86 RPM
SRP007412_cerebellum	1.39 RPM	106.64 RPM
SRP007412_heart	0.00 RPM	69.36 RPM
SRP007412_kidney	0.29 RPM	56.44 RPM
SRP007412_liver	0.05 RPM	27.14 RPM
SRP007412_testis	0.73 RPM	50.50 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_393 was not detected

EST

No EST(s) were mapped for retro_mmus_393 retrocopy.

TSS

No TSS is located nearby retro_mmus_393 retrocopy 5' end.

Lab

retro_mmus_393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_393 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002637	1 retrocopy	retro_amel_1655,
Dasypus novemcinctus	ENSDNOG00000006963	1 retrocopy	retro_dnov_1829,
Felis catus	ENSFCAG00000028088	1 retrocopy	retro_fcat_1789,
Myotis lucifugus	ENSMLUG00000015591	1 retrocopy	retro_mluc_1131,
Mus musculus	ENSMUSG00000056820	1 retrocopy	retro_mmus_393 ,
Otolemur garnettii	ENSOGAG00000005575	1 retrocopy	retro_ogar_91,
Ictidomys tridecemlineatus	ENSSTOG00000024989	1 retrocopy	retro_itri_259,