RetrogeneDB ID: retro_mmus_2396

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:129899092..129899899(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000070729
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Srsf5
• Ensembl ID: ENSMUSG00000021134
• Aliases: Srsf5, Sfrs5
• Description: serine/arginine-rich splicing factor 5 [Source:MGI Symbol;Acc:MGI:98287]

Sequence

>retro_mmus_2396
ATGAGTGGCTGTCGAGTGTTCATTGGGAGACTAAATCCAGCAGCGAGGGTGAAAGATGTGGAAAGATTCTTCAAGGGTTA
CGGACGGATCCGAGATATTGACTTGAAAACAGGTTTTGGTTTTGTGGAATTTGAGGACCCAAGGGATGCAGATGATGCTG
TTTATGAACTTGATGGGAAGGAACTTTGCAGTGAAAGGGTGACGATTGAACATGCTCGGGCTCGATCTCGAGGTGGAAGA
GGTAGAGGACGATACTCCGACCGTTTTAGCAGTCGCAGACCTCGAAATGATAGACGAAATGCTCCACCTGTAAGAACAGA
AAATCGACTTATAGTTGAGAATTTATCCTCAAGAGTCAGCTGGCAGGATCTCAAAGATTTCATGAGACAAGCTGGGGAAG
TAACCTTTGCGGATGCACATCGACCTAAACTAAATGAAGGGGTAGTTGAGTTTGCCTCTTATGGTGACTTAAAGAATGCT
ATTGAGAAACTTTCTGGAAAGGAAATTAACGGGAGAAAAATCAAATTAATTGTAGGCAGCAAAAGGCACAGGTCAAGAAG
CAGGTCACGATCTCGGACCAGGAGTTCCTCTAGGTCCCGTAGCCGATCCCGTTCACGCAGGAGCAAGTCTTACAGCCGAT
CAAGGAGCAGGAGCCGGAGCCAGAGCAAGTCCCGTTCTGGTAGTAGGTCTCCTGTGCCTGAGAAGAGCCAGAAACGTGGT
TCTTCGAGTAGATCTAAATCTCCAGCATCTGTGGATCGCCAGAGGTCCCGATCCCGGTCCAGGTCCAGATCAGTTGACAG
TGGCAAT

Alignment

ORF - retro_mmus_2396 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGCRVFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFEDPRDADDAVYELDGKELCSERVTIE
          MSGCRVFIGRLNPAAR.KDVERFFKGYGRIRDIDLK.GFGFVEFEDPRDADDAVYELDGKELCSERVTIE
Retrocopy MSGCRVFIGRLNPAARVKDVERFFKGYGRIRDIDLKTGFGFVEFEDPRDADDAVYELDGKELCSERVTIE

Parental  HARARSRGGRGRGRYSDRFSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAH
          HARARSRGGRGRGRYSDRFSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAH
Retrocopy HARARSRGGRGRGRYSDRFSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAH

Parental  RPKLNEGVVEFASYGDLKNAIEKLSGKEINGRKIKLIEGSKRHRSRSRSRSRTRSSSRSRSRSRSRRSKS
          RPKLNEGVVEFASYGDLKNAIEKLSGKEINGRKIKLI.GSKRHRSRSRSRSRTRSSSRSRSRSRSRRSKS
Retrocopy RPKLNEGVVEFASYGDLKNAIEKLSGKEINGRKIKLIVGSKRHRSRSRSRSRTRSSSRSRSRSRSRRSKS

Parental  YSRSRSRSRSRSKSRSGSRSPVPEKSQKRGSSSRSKSPASVDRQRSRSRSRSRSVDSGN
          YSRSRSRSRS.SKSRSGSRSPVPEKSQKRGSSSRSKSPASVDRQRSRSRSRSRSVDSGN
Retrocopy YSRSRSRSRSQSKSRSGSRSPVPEKSQKRGSSSRSKSPASVDRQRSRSRSRSRSVDSGN

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	0.49 RPM	187.91 RPM
SRP007412_cerebellum	0.69 RPM	258.44 RPM
SRP007412_heart	0.56 RPM	169.91 RPM
SRP007412_kidney	1.15 RPM	219.93 RPM
SRP007412_liver	0.55 RPM	161.31 RPM
SRP007412_testis	0.69 RPM	176.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2396 was not detected

EST

No EST(s) were mapped for retro_mmus_2396 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_100852	260 libraries	492 libraries	315 libraries	1 library	4 libraries

The graphical summary, for retro_mmus_2396 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_2396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001521	2 retrocopies	retro_meug_1173, retro_meug_2182,
Monodelphis domestica	ENSMODG00000011362	1 retrocopy	retro_mdom_934,
Mus musculus	ENSMUSG00000021134	1 retrocopy	retro_mmus_2396 ,
Mus musculus	ENSMUSG00000024097	1 retrocopy	retro_mmus_3288,
Mus musculus	ENSMUSG00000071172	9 retrocopies	retro_mmus_100, retro_mmus_1347, retro_mmus_1749, retro_mmus_2294, retro_mmus_2337, retro_mmus_2433, retro_mmus_2654, retro_mmus_2933, retro_mmus_3629,
Rattus norvegicus	ENSRNOG00000005513	1 retrocopy	retro_rnor_2900,
Tupaia belangeri	ENSTBEG00000001972	1 retrocopy	retro_tbel_2707,