RetrogeneDB ID: retro_mmus_1550

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:16889722..16890458(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccnb1
• Ensembl ID: ENSMUSG00000041431
• Aliases: Ccnb1, Ccnb1-rs1, Ccnb1-rs13, CycB1, Cycb-4, Cycb-5, Cycb1-rs1
• Description: cyclin B1 [Source:MGI Symbol;Acc:MGI:88302]

Sequence

>retro_mmus_1550
AAGTCCAATGGATGTGTGCCTGCAGAAGAGTATCTGTGTCAGGCTTTCTCTGATGTAATCCTTGCAGTGAATAACGTAGA
CGCAGATGATGGAGCTGACCCAAACCTCTGTAGTGAATATGTGAAAGATGTCTATGCTTATCTCAGACAACTGGAGGAAG
AGCAGTCAGTTAGACCAAAATACCTACAGGGTCTGAAGTGACTAGAAATATGAGAGCTATCCTCATTGACTGGCTAATAC
AGGTTCAGATGAAATTTAGGCTGCTTCAGGAGACCATGTTTATGACTGTGTCCATTATTGATCGGTTCATGCAGAACAGT
TGTGTACCCAAGAAGATGCTGCAGCTGGTCGGTGTAACTGCTATGTTTATTGCAAGCAAATATGAGATGTACCCTCCAGA
AATAGGTGACTTCGCCTTTGTGACTAACAACACTTAGCTAAGCACCAGATCAGACAGATGGAGATGAAGATTCTCAGAGT
TCTGAACTTCAGTCTAGGTCTCCCTCTGCCTCTGCCCTTCCTCCACAGAGCATCTAAAGTCGGAGAGGTTGACATCGAGC
AGCACACTTTGGCCAAATACCTCATGGAGCTCTCCATGCTGGACTACAAAATGGTTCATTTTGCTCCTTCTCAAATTGCA
GCTGGGGCTTTCAGCTTAGCGCTGAAAATTTTTGACAACAGTGAATGGGTAAGCTGTCTCACCAAACTACCAAGCATTCG
AATGGACCACTTGGTA

Alignment

ORF - retro_mmus_1550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.94 %
• Parental protein coverage: 57.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETSGCAPAEEYLCQAFSDVILAVSDVDADDGADPNLCSEYVKDIYAYLRQLEEEQSVRPKYLQG-REVTG
          ...GC.PAEEYLCQAFSDVILAV..VDADDGADPNLCSEYVKD.YAYLRQLEEEQSVRPKYLQG..EVT.
Retrocopy KSNGCVPAEEYLCQAFSDVILAVNNVDADDGADPNLCSEYVKDVYAYLRQLEEEQSVRPKYLQG<SEVTR

Parental  NMRAILIDWLIQVQMKFRLLQETMYMTVSIIDRFMQNSCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDF
          NMRAILIDWLIQVQMKFRLLQETM.MTVSIIDRFMQNSCVPKKMLQLVGVTAMFIASKYE.MYPPEIGDF
Retrocopy NMRAILIDWLIQVQMKFRLLQETMFMTVSIIDRFMQNSCVPKKMLQLVGVTAMFIASKYE-MYPPEIGDF

Parental  AFVTNNT-YTKHQIRQMEMKILRVLNFSLGRPLPLHFLRRASKVGEVDVEQHTLAKYLMELSMLDYDMVH
          AFVTNNT...KHQIRQMEMKILRVLNFSLG.PLPL.FL.RASKVGEVD.EQHTLAKYLMELSMLDY.MVH
Retrocopy AFVTNNT<LAKHQIRQMEMKILRVLNFSLGLPLPLPFLHRASKVGEVDIEQHTLAKYLMELSMLDYKMVH

Parental  FAPSQIAAGAFCLALKILDNGEWTPTLQHYLSYSEDSLL
          FAPSQIAAGAF.LALKI.DN.EW...L....S...D.L.
Retrocopy FAPSQIAAGAFSLALKIFDNSEWVSCLTKLPSIRMDHLV

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	0.56 RPM
SRP007412_cerebellum	0.00 RPM	0.09 RPM
SRP007412_heart	0.00 RPM	0.28 RPM
SRP007412_kidney	0.02 RPM	0.40 RPM
SRP007412_liver	0.00 RPM	0.11 RPM
SRP007412_testis	0.00 RPM	28.54 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1550 was not detected

EST

No EST(s) were mapped for retro_mmus_1550 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_50568	682 libraries	166 libraries	184 libraries	35 libraries	5 libraries

The graphical summary, for retro_mmus_1550 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_1550 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1550 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
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000034165	1 retrocopy	retro_mmus_2519,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550 , retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,