RetrogeneDB ID: retro_mmus_2064

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:97948986..97949679(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082820
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2064
ATGGGGAAGTCATTCGCCAATTTCATGTGTAAGAAGGACTTCCATCCTGCGTCCAAATCCAACATCAAGAAGGTATGGAT
GGCAGAACAGAAAATATCGTATGATAAAAAGAAACAAGAAGAATTAATGCAACAGTACCTTAAAGAGCAGGAGTCGTATG
ATAACAGATTGCTTATGGGAGATGAACGTGTGAAGAATGGACTGAATTTCATGTACGAGGCCCCACCAGGAGTTAAGAAA
GAAAACAAAGAGAAAGAAGAAACAGAAGGAGAGACCGAGTACAAGTTTGAATGGCAGAAAGGCGCTCCGAGAGAAAAATA
TGTCAAAGATGACATGAACATCAGAGATCAGCCCTTTGGTATTCAGGTTCGAAATGTAAGGTGTATTAAATGTCACAAGT
GGGGCCATGTGAACACAGATTGAGAGTGTCCCTTGTTTGGTCTTTCTGGGATCAATGCAAGTTCAGTTCCTACTGATGGC
TCAGGGCCGTAGATGCACCCCTCGGAGCTAATAGCGGAGATGAGAAACAGTGGGTTTGCACTAAAACGAAATGTACTGGG
GAGAAACTTGACCGCAAATGATCCATCACAGGCCTATGTCGCAAGTGACTGTGAAGAAGACCCTGAAGTTGAGTTCTTAA
AGTCGCTCACCACCAAGCAGAAGCAGAAGCTCCTCAGGAAATTGGATAGACTT

Alignment

ORF - retro_mmus_2064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.21 %
• Parental protein coverage: 51.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKSFANFMCKKDFHPASKSNIKKVWMAEQKISYDKKKQEELMQQYLKEQESYDNRLLMGDERVKNGLNF
          MGKSFANFMCKKDFHPASKSNIKKVWMAEQKISYDKKKQEELMQQYLKEQESYDNRLLMGDERVKNGLNF
Retrocopy MGKSFANFMCKKDFHPASKSNIKKVWMAEQKISYDKKKQEELMQQYLKEQESYDNRLLMGDERVKNGLNF

Parental  MYEAPPGVKKENKEKEETEGETEYKFEWQKGAPREKYAKDDMNIRDQPFGIQVRNVRCIKCHKWGHVNTD
          MYEAPPGV..............EYKFEWQKGAPREKY.KDDMNIRDQPFGIQVRNVRCIKCHKWGHVNTD
Retrocopy MYEAPPGVXXXXXXXXXXXXXXEYKFEWQKGAPREKYVKDDMNIRDQPFGIQVRNVRCIKCHKWGHVNTD

Parental  RECPLFGLSGINASSVPTDGSGPSMHPSELIAEMRNSGFALKRNVLGRNLTANDPSQDYVASDCEEDPEV
          .ECPLFGLSGINASSVPTDGSGP.MHPSELIAEMRNSGFALKRNVLGRNLTANDPSQ.YVASDCEEDPEV
Retrocopy *ECPLFGLSGINASSVPTDGSGP*MHPSELIAEMRNSGFALKRNVLGRNLTANDPSQAYVASDCEEDPEV

Parental  EFLKSLTTKQKQKLLRKLDRL
          EFLKSLTTKQKQKLLRKLDRL
Retrocopy EFLKSLTTKQKQKLLRKLDRL

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	0.09 RPM	8.38 RPM
SRP007412_heart	0.09 RPM	3.70 RPM
SRP007412_kidney	0.10 RPM	6.87 RPM
SRP007412_liver	0.14 RPM	4.67 RPM
SRP007412_testis	0.50 RPM	27.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2064 was not detected

EST

No EST(s) were mapped for retro_mmus_2064 retrocopy.

TSS

No TSS is located nearby retro_mmus_2064 retrocopy 5' end.

Lab

retro_mmus_2064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2064 has 0 orthologous retrocopies within eutheria group .

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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,