RetrogeneDB ID: retro_mmus_244

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:39358257..39358905(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000050533
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Cflar
• Ensembl ID: ENSMUSG00000026031
• Aliases: Cflar, 2310024N18Rik, A430105C05Rik, CLARP, Cash, Casper, ENSMUSG00000072980, FLAME, FLAME-1, Flip, Gm9845, I-FLICE, MRIT, c-Flip
• Description: CASP8 and FADD-like apoptosis regulator [Source:MGI Symbol;Acc:MGI:1336166]

Sequence

>retro_mmus_244
ATGGCCCAGAGCCCTGTGTCTGCCGAGGTCATTCACCAGGTGGAAGAGTGTCTTGATGAAGACGAGAAGGAGATGATGCT
CTTCCTGTGTAGAGATGTGACTGAGAACCTGGCTGCACCTAACGTCAGGGACCTCCTGGATAGCTTAAGTGAGAGAGGCC
AGCTCTCTTTTGCTACCTTGGCTGAATTGCTCTACAGAGTGAGGCGGTTTGACCTTCTCAAGAGGATCTTGAAGACAGAC
AAAGCAACCGTGGAGGACCACCTGCGCAGAAACCCTCACCTGGTTTCTGATTATAGGGTCCTGCTGATGGAGATTGGTGA
GAGCTTAGATCAGAACGATGTATCCTCCTTAGTTTTCCTTACAAGGGATTACACAGGCAGAGGCAAGATAGCCAAGGACA
AGAGTTTCTTGGATCTGGTGATTGAATTGGAGAAACTGAATCTAATTGCTTCAGACCAATTGAATTTGTTAGAAAAATGC
CTGAAGAACATCCACAGAATAGACTTGAACACAAAGATCCAGAAGTACACCCAGTCCAGCCAAGGAGCAAGATCAAATAT
GAATACTCTCCAGGCTTCGCTCCCAAAATTGAGTATCAAGTATAACTCAAGGGTGAGTCTGGAGCCAGTGTATGGAGTAC
CAGCATGA

Alignment

ORF - retro_mmus_244 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAQSPVSAEVIHQVEECLDEDEKEMMLFLCRDVTENLAAPNVRDLLDSLSERGQLSFATLAELLYRVRRF
          MAQSPVSAEVIHQVEECLDEDEKEMMLFLCRDVTENLAAPNVRDLLDSLSERGQLSFATLAELLYRVRRF
Retrocopy MAQSPVSAEVIHQVEECLDEDEKEMMLFLCRDVTENLAAPNVRDLLDSLSERGQLSFATLAELLYRVRRF

Parental  DLLKRILKTDKATVEDHLRRNPHLVSDYRVLLMEIGESLDQNDVSSLVFLTRDYTGRGKIAKDKSFLDLV
          DLLKRILKTDKATVEDHLRRNPHLVSDYRVLLMEIGESLDQNDVSSLVFLTRDYTGRGKIAKDKSFLDLV
Retrocopy DLLKRILKTDKATVEDHLRRNPHLVSDYRVLLMEIGESLDQNDVSSLVFLTRDYTGRGKIAKDKSFLDLV

Parental  IELEKLNLIASDQLNLLEKCLKNIHRIDLNTKIQKYTQSSQGARSNMNTLQASLPKLSIKYNSRVSLEPV
          IELEKLNLIASDQLNLLEKCLKNIHRIDLNTKIQKYTQSSQGARSNMNTLQASLPKLSIKYNSRVSLEPV
Retrocopy IELEKLNLIASDQLNLLEKCLKNIHRIDLNTKIQKYTQSSQGARSNMNTLQASLPKLSIKYNSRVSLEPV

Parental  YGVPA
          YGVPA
Retrocopy YGVPA

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	18.85 RPM
SRP007412_cerebellum	0.00 RPM	23.10 RPM
SRP007412_heart	0.03 RPM	48.13 RPM
SRP007412_kidney	0.08 RPM	130.47 RPM
SRP007412_liver	0.05 RPM	127.07 RPM
SRP007412_testis	0.00 RPM	10.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_244 was not detected

EST

No EST(s) were mapped for retro_mmus_244 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_94690	572 libraries	416 libraries	77 libraries	6 libraries	1 library

The graphical summary, for retro_mmus_244 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_244 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_244 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004505	1 retrocopy	retro_cjac_3235,
Monodelphis domestica	ENSMODG00000015097	1 retrocopy	retro_mdom_1986,
Mus musculus	ENSMUSG00000026031	1 retrocopy	retro_mmus_244 ,