RetrogeneDB ID: retro_mmus_1827

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:37860703..37860901(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Deb1
• Ensembl ID: ENSMUSG00000032526
• Aliases: Deb1, 1110020I04Rik, AI463209, Ss18l2
• Description: differentially expressed in B16F10 1 [Source:MGI Symbol;Acc:MGI:1349474]

Sequence

>retro_mmus_1827
GGCAAGGTCAAAGTCAACCAGGAGACCATCCTGTGGCTCCTGGGGAAAATGCCCAGCTGGTCTGCTGTTTCCTGGATTAT
CAGAACCAGGGCAGAGTGAGCAAGTGTGCACAATTGCCAATGTGTGTTCCACAGAAGTCTCATTTCTTTAGCTGCCGTTG
TGGATGCCGACATGACCAGTGCTTCAGAGGCAGTGGAG

Alignment

ORF - retro_mmus_1827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.41 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKAKVNQETIQRLL-EENDQLIRCIVEYQNKGRANECVQY-QHVLHRNLIYLATIADANTSSLTKAVE
          GK.KVNQETI..LL..EN.QL..C...YQN.GR...C.Q..Q.V.HR.LI.LA...DA...S...AVE
Retrocopy GKVKVNQETILWLL<GENAQLVCCFLDYQNQGRVSKCAQL>QCVFHRSLISLAAVVDADMTSASEAVE

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	14.72 RPM
SRP007412_cerebellum	0.00 RPM	13.24 RPM
SRP007412_heart	0.00 RPM	26.49 RPM
SRP007412_kidney	0.00 RPM	15.40 RPM
SRP007412_liver	0.00 RPM	16.30 RPM
SRP007412_testis	0.00 RPM	1.65 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1827 was not detected

EST

No EST(s) were mapped for retro_mmus_1827 retrocopy.

TSS

No TSS is located nearby retro_mmus_1827 retrocopy 5' end.

Lab

retro_mmus_1827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1827 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000989	1 retrocopy	retro_acar_189,
Dipodomys ordii	ENSDORG00000015005	4 retrocopies	retro_dord_286, retro_dord_39, retro_dord_643, retro_dord_658,
Erinaceus europaeus	ENSEEUG00000014065	1 retrocopy	retro_eeur_634,
Echinops telfairi	ENSETEG00000007192	2 retrocopies	retro_etel_1749, retro_etel_2074,
Loxodonta africana	ENSLAFG00000021542	2 retrocopies	retro_lafr_754, retro_lafr_92,
Myotis lucifugus	ENSMLUG00000013024	1 retrocopy	retro_mluc_21,
Mus musculus	ENSMUSG00000032526	3 retrocopies	retro_mmus_1247, retro_mmus_1827 , retro_mmus_3284,
Mus musculus	ENSMUSG00000037013	1 retrocopy	retro_mmus_1951,
Ochotona princeps	ENSOPRG00000015198	4 retrocopies	retro_opri_401, retro_opri_516, retro_opri_542, retro_opri_593,
Sorex araneus	ENSSARG00000014056	1 retrocopy	retro_sara_465,
Tarsius syrichta	ENSTSYG00000007658	1 retrocopy	retro_tsyr_1687,