RetrogeneDB ID: retro_mmus_3104

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:5117360..5118052(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cir1
• Ensembl ID: ENSMUSG00000041777
• Aliases: None
• Description: corepressor interacting with RBPJ, 1 [Source:MGI Symbol;Acc:MGI:1914185]

Sequence

>retro_mmus_3104
ATGGGGAAGTCATTCACCAATTTCATGTGTAAGAAGGATTTCCATCCTGTGTCCAAATCCAACATCAAGAAGGTATGGAT
GGCAGAACAGAAAATATCGTATGATAAAAAGAAACAAGAAGAATTAATGCAACAGTACCTTAAAGAGCAGGAGTCGTATG
ATAACAGATTGCTCATGGGAGATGAGCATGTGAAAAATGGCCTGAATTTCATGTACGAGGCCCCGCCAGGAGTTAAGAAA
GAAAACAAAGAGAAAGAAGAAACGGAAGGAGAGACCGAGTACAAGTTTGAATGGCAGAAAGGCACTCTGAGAGAAAAATA
TGCCAAAGATGACATGAACATCAGAGATCAGCCCTTTGGTATTCAGGTTCGAAATGTAAGGTGTATTAAATGTCACAAGT
GGGGCCACGTGAACACAGATCGAGAGTGTCCCTTGTTTGGTCTTTCTGGAATCAATGCAAGTTCAGTTCCTATTGTGGCT
CAGGGACGTCGATGCATGCCTCGGATCTAATAGCGGAGATGAGAAACAGTGGGTTTGCACTGAAACGAAATGTACTGGGG
AGAAACTAGACCACAAATGATCCATCACAGGACTATGTCGGAAGTGACTGTGAAGAAGACCCTGAAGTTGAATTCTTAAA
GTCGCCCACCACCAAGCAGAAGCAGAAGCTCCTCAGGAAATTGGATAGACTT

Alignment

ORF - retro_mmus_3104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.53 %
• Parental protein coverage: 51.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKSFANFMCKKDFHPASKSNIKKVWMAEQKISYDKKKQEELMQQYLKEQESYDNRLLMGDERVKNGLNF
          MGKSF.NFMCKKDFHP.SKSNIKKVWMAEQKISYDKKKQEELMQQYLKEQESYDNRLLMGDE.VKNGLNF
Retrocopy MGKSFTNFMCKKDFHPVSKSNIKKVWMAEQKISYDKKKQEELMQQYLKEQESYDNRLLMGDEHVKNGLNF

Parental  MYEAPPGVKKENKEKEETEGETEYKFEWQKGAPREKYAKDDMNIRDQPFGIQVRNVRCIKCHKWGHVNTD
          MYEAPPGVKKENKEKEETEGETEYKFEWQKG..REKYAKDDMNIRDQPFGIQVRNVRCIKCHKWGHVNTD
Retrocopy MYEAPPGVKKENKEKEETEGETEYKFEWQKGTLREKYAKDDMNIRDQPFGIQVRNVRCIKCHKWGHVNTD

Parental  RECPLFGLSGINASSVPT-DGSGPSMHPSELIAEMRNSGFALKRNVLGRNLTANDPSQDYVASDCEEDPE
          RECPLFGLSGINASSVP...GSG.SMH.S.LIAEMRNSGFALKRNVLGRN.T.NDPSQDYV.SDCEEDPE
Retrocopy RECPLFGLSGINASSVPI<CGSGTSMHASDLIAEMRNSGFALKRNVLGRN*TTNDPSQDYVGSDCEEDPE

Parental  VEFLKSLTTKQKQKLLRKLDRL
          VEFLKS.TTKQKQKLLRKLDRL
Retrocopy VEFLKSPTTKQKQKLLRKLDRL

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	0.12 RPM	5.30 RPM
SRP007412_cerebellum	0.17 RPM	8.38 RPM
SRP007412_heart	0.16 RPM	3.70 RPM
SRP007412_kidney	0.19 RPM	6.87 RPM
SRP007412_liver	0.08 RPM	4.67 RPM
SRP007412_testis	0.82 RPM	27.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3104 was not detected

EST

No EST(s) were mapped for retro_mmus_3104 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_142721	603 libraries	330 libraries	133 libraries	4 libraries	2 libraries
TSS #2	TSS_142722	561 libraries	257 libraries	220 libraries	27 libraries	7 libraries

The graphical summary, for retro_mmus_3104 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_3104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3104 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007884	1 retrocopy	retro_cjac_2152,
Homo sapiens	ENSG00000138433	2 retrocopies	retro_hsap_3082, retro_hsap_3394,
Macaca mulatta	ENSMMUG00000023006	1 retrocopy	retro_mmul_1967,
Mustela putorius furo	ENSMPUG00000013943	1 retrocopy	retro_mputfur_178,
Mus musculus	ENSMUSG00000041777	2 retrocopies	retro_mmus_2064, retro_mmus_3104 ,
Nomascus leucogenys	ENSNLEG00000005869	3 retrocopies	retro_nleu_1540, retro_nleu_2013, retro_nleu_2691,
Pan troglodytes	ENSPTRG00000012652	2 retrocopies	retro_ptro_2079, retro_ptro_2306,