RetrogeneDB ID: retro_mmus_672

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:108699219..108700092(-)
• Located in intron of: ENSMUSG00000035864

Retrocopy information

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

Parental gene information

• Parental gene symbol: Brcc3
• Ensembl ID: ENSMUSG00000031201
• Aliases: Brcc3, C6.1A
• Description: BRCA1/BRCA2-containing complex, subunit 3 [Source:MGI Symbol;Acc:MGI:2389572]

Sequence

>retro_mmus_672
ATGGCGGTGCGGATGATGCAGGGAGTGCAGGCGGTTTACCTTGAATCGGACGCTTTCCTGGTTTGTCTCAATCACGCTCT
GAGCACAGAGAAGGAGGAAGTGATGGGTCTGTGTATAGGGCAGTTGAATGATCACGGGAGGAGTGACTCCAGGCTTGCAT
ACGCTGGAGCTGAGATGTGCACAGTTGCGAAAAAGATGGAGGCCACCAGAATTGTTCACATTCATTCTGTTATTATCTTG
CGACGTTCTGACAAGACAAAGGACCGGGTAGAAATATCTCCGGAGCAACTGTCTGCAGCCTCGATAGAGGCAGAACGGTT
AGCAGAGCAAACAGGTCGTCCCATGAGAGTTGTGGGCTGGTACCATTCCCACCCTCATATAACCGTTTGGCCTTCTCATG
TCGACGTGCGTACACAGGCCATGTACCAGATGATGGATCAGAGCTTTGTAGGACTGATCTTTGCTTGTTTCATAGAAGAC
AAACCCACAAAGATAGGCCGTGTACTCTATACTTGCTTCCAGTCTGTACAAGCATCGAAGAGTTCAGAATATGAGAGACT
TGAAATCCCAATCCATATTGTACCTCGTACCACCATCGGGACAGTATGCCTCAGGTCAGCCATAGAGCTGCCGGGGATCC
TATGTCAGGAAGAACAAGAGGCATATAGGAGGATTCACGGCCTTACACATCTGGACTCAGTAACTAAGATCCATAATGGC
TCTGTATTCACCAAGCATCTGTGCAGTCAGATGTCCGCGGTCTGTGGGCCTCTCCTACAGTGGTTGGAGGACAGACTAGA
GCAAAACCAGCAGCGTTTGCAGGAGTTGGAACAAGAAAAGGAAGACCTTATGGAAGAGCTGTCTTCCCTAGAA

Alignment

ORF - retro_mmus_672 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVQVVQAVQAVHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDIRSDSKFTYTGTEMRTVQEKMDTIR
          MAV...Q.VQAV.LESDAFLVCLNHALSTEKEEVMGLCIG.LND..RSDS...Y.G.EM.TV..KM...R
Retrocopy MAVRMMQGVQAVYLESDAFLVCLNHALSTEKEEVMGLCIGQLNDHGRSDSRLAYAGAEMCTVAKKMEATR

Parental  IVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQA
          IVHIHSVIILRRSDK.KDRVEISPEQLSAAS.EAERLAE.TGRPMRVVGWYHSHPHITVWPSHVDVRTQA
Retrocopy IVHIHSVIILRRSDKTKDRVEISPEQLSAASIEAERLAEQTGRPMRVVGWYHSHPHITVWPSHVDVRTQA

Parental  MYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSSEYERIEIPIHIVPHITIGKVCLESAVEL
          MYQMMDQ.FVGLIF.CFIEDK.TK.GRVLYTCFQS.QA.KSSEYER.EIPIHIVP..TIG.VCL.SA.EL
Retrocopy MYQMMDQSFVGLIFACFIEDKPTKIGRVLYTCFQSVQASKSSEYERLEIPIHIVPRTTIGTVCLRSAIEL

Parental  PKILCQEEQDAYRRIHSLTHLDSVTKIHNGSVFTKNLCSQMSAVSGPLLQWLEDRLEQNQQHLQELQQEK
          P.ILCQEEQ.AYRRIH.LTHLDSVTKIHNGSVFTK.LCSQMSAV.GPLLQWLEDRLEQNQQ.LQEL.QEK
Retrocopy PGILCQEEQEAYRRIHGLTHLDSVTKIHNGSVFTKHLCSQMSAVCGPLLQWLEDRLEQNQQRLQELEQEK

Parental  EELMEELSSLE
          E.LMEELSSLE
Retrocopy EDLMEELSSLE

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	0.23 RPM	27.26 RPM
SRP007412_cerebellum	0.04 RPM	24.49 RPM
SRP007412_heart	0.00 RPM	18.83 RPM
SRP007412_kidney	0.00 RPM	28.03 RPM
SRP007412_liver	0.03 RPM	16.14 RPM
SRP007412_testis	10.84 RPM	2.61 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_672 was not detected

EST

No EST(s) were mapped for retro_mmus_672 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_212	1054 libraries	14 libraries	0 libraries	1 library	3 libraries

The graphical summary, for retro_mmus_672 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_672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_672 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007817	2 retrocopies	retro_btau_1327, retro_btau_1646,
Cavia porcellus	ENSCPOG00000001882	2 retrocopies	retro_cpor_388, retro_cpor_627,
Homo sapiens	ENSG00000185515	1 retrocopy	retro_hsap_3271,
Gorilla gorilla	ENSGGOG00000027248	1 retrocopy	retro_ggor_2226,
Monodelphis domestica	ENSMODG00000016487	1 retrocopy	retro_mdom_930,
Mus musculus	ENSMUSG00000031201	1 retrocopy	retro_mmus_672 ,
Nomascus leucogenys	ENSNLEG00000014460	1 retrocopy	retro_nleu_2940,
Sarcophilus harrisii	ENSSHAG00000005392	1 retrocopy	retro_shar_51,
Ictidomys tridecemlineatus	ENSSTOG00000019781	2 retrocopies	retro_itri_1271, retro_itri_806,