RetrogeneDB ID: retro_mmus_1255

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:21011002..21011299(-)
• Located in intron of: ENSMUSG00000021823

Retrocopy information

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

Parental gene information

• Parental gene symbol: 3830406C13Rik
• Ensembl ID: ENSMUSG00000033111
• Aliases: None
• Description: RIKEN cDNA 3830406C13 gene [Source:MGI Symbol;Acc:MGI:1917937]

Sequence

>retro_mmus_1255
ATGGCTTCCTTGTTTACTCAAGAAATTCACCTTTCTAAAAGACATGAAGAAATAGTATCACAAAGATTAATGTTACTTCA
GAAAATGAAAAACAAATTTGGAGATGAAAACACAGAAAGGGCATCTCTCCTCCAAGCCACTGAGACTGCTTCTAGAAGAA
ACCTCCGACTCTTGCAGGACATAGATGCTGCAGAGGAGGCTTTTCAGACCAAGCTTATCCCACACCCACAGCCTTCGATG
CTTTCTCTTGAGACTCGTTACTGGGCATCAGTAGAAGAACATATCCCCAAGTGGGAA

Alignment

ORF - retro_mmus_1255 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.98 %
• Parental protein coverage: 77.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASLFTQEIHLSKRHEEILSQRLMLLQKMKNKFGDENTERASLLQATETASRRNLRLLKDIDAAEEAFQT
          MASLFTQEIHLSKRHEEI.SQRLMLLQKMKNKFGDENTERASLLQATETASRRNLRLL.DIDAAEEAFQT
Retrocopy MASLFTQEIHLSKRHEEIVSQRLMLLQKMKNKFGDENTERASLLQATETASRRNLRLLQDIDAAEEAFQT

Parental  KLIPHPQPSMLSLETRYWASVEEHIPKWE
          KLIPHPQPSMLSLETRYWASVEEHIPKWE
Retrocopy KLIPHPQPSMLSLETRYWASVEEHIPKWE

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	15.61 RPM
SRP007412_cerebellum	0.00 RPM	8.99 RPM
SRP007412_heart	0.00 RPM	9.09 RPM
SRP007412_kidney	0.00 RPM	14.90 RPM
SRP007412_liver	0.00 RPM	7.24 RPM
SRP007412_testis	0.00 RPM	29.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1255 was not detected

EST

No EST(s) were mapped for retro_mmus_1255 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_33246	256 libraries	414 libraries	395 libraries	5 libraries	2 libraries

The graphical summary, for retro_mmus_1255 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_1255 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1255 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015374	1 retrocopy	retro_amel_1312,
Canis familiaris	ENSCAFG00000007123	1 retrocopy	retro_cfam_1485,
Choloepus hoffmanni	ENSCHOG00000004965	7 retrocopies	retro_chof_138, retro_chof_2082, retro_chof_423, retro_chof_536, retro_chof_659, retro_chof_73, retro_chof_96,
Erinaceus europaeus	ENSEEUG00000000474	1 retrocopy	retro_eeur_656,
Felis catus	ENSFCAG00000027983	1 retrocopy	retro_fcat_577,
Macropus eugenii	ENSMEUG00000013085	2 retrocopies	retro_meug_1990, retro_meug_2091,
Microcebus murinus	ENSMICG00000016406	1 retrocopy	retro_mmur_461,
Mustela putorius furo	ENSMPUG00000016914	1 retrocopy	retro_mputfur_751,
Mus musculus	ENSMUSG00000033111	1 retrocopy	retro_mmus_1255 ,
Otolemur garnettii	ENSOGAG00000008107	2 retrocopies	retro_ogar_484, retro_ogar_485,
Tupaia belangeri	ENSTBEG00000017312	1 retrocopy	retro_tbel_1713,