RetrogeneDB ID: retro_mmus_2730

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:47045155..47046286(+)
• Located in intron of: ENSMUSG00000039419

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccni
• Ensembl ID: ENSMUSG00000063015
• Aliases: None
• Description: cyclin I [Source:MGI Symbol;Acc:MGI:1341077]

Sequence

>retro_mmus_2730
ATGAAGATTCCAGGACCTTTGGAAAGCCAGAGATTGTTTTTTTGTTGGAAAGGGCAATCTCCAGGGAAGCCCAGATGTGG
AAGGTGAATGTGCCGAAAATACCTACAAATCAGAATGTTTCTCCATCCCAGAGAGATGAAGTAATTCAATGGTTGGCCAA
ATTCAAATACCAGTTCAACCTCTATCCAGAAACATTTGCTCTGGCAAGCAGTCTTTTGGATAGGATTTTAGCTACAGTAA
AAGCCCATCCAAAATATTTGAATTATATTGCAATCAGCTGGTTTTTTCTGGCTGCTAAGACTGTTGAGGAAGATGAGAAA
ATTCCAGTGCTAAAGGTATTGGCAAGAGACAGTTTCTGTGGGTGTTCCTCATCTGAGATTTTGAGAATGGAGAGAATTAT
TCTGGATAAATTGAATTGGGATCTTCACATGGCCACACCATTGGATTTTCTTCACATTTTCCATGCCATTGTGGTGTCAA
CTAGGCCTCAGTTACTTTTCAGTTGGCCCAAATTGAGCCCATCTCAACATTTGGTAATCCTGACCAAAAAGCTGCTTCCC
TGTATGGCCTGCAACCAACTTCTGCAGTTCAAAGGGTCCATGCTGGCTCTGGCCATGGTTAGTCTGGAAATGGAGAAACC
CATTCCTGATTGGCTTCCTCTTACGATTGAACTGCTTCAGGAAGCAGAGATGGGCAGCTCCCAGTAGATCCACTGCCGGG
GAGCTGGTGGCATATCACTGTTCTGCTCCGCAGTCTGCCCTGCCTCTAAATTCCGTTTATGTCTACCGTCCCCTCAAGCA
CACCCTGGTAACCTGTGACAAAGGAGCATTCACATTACATCCCTCCTCTGTCTCAGGCCCAGATTTCTCCAAGGACAAGA
GCAAGCCAGAAGTGCCAGTCCGAGGTCCAGCAGCCTTCCACCTGCATCTCCCCGCTGCCAGTGGGTGCAAGCAAACCTCT
GCTAAATGGAAAGTGGAGGAGATGGAGGTGGATGACTTCTCCAATGGGATCAAGCCGCTCTATAATGAGGACAATGGTCC
TGAGAATGTGGGTTCTGTATGTGGCACTGATTTATCAAGGCAAGAGGGCCATGCTTCCCCCTGTCCACCTTTGCAGCCTG
TTTCTGTCATG

Alignment

ORF - retro_mmus_2730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKFPGPLENQRLSS-LLERAISREAQMWKVNVPKIPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALA
          MK.PGPLE.QRL...LLERAISREAQMWKVNVPKIPTNQNVSPSQRDEVIQWLAK.KYQFNLYPETFALA
Retrocopy MKIPGPLESQRLFF<LLERAISREAQMWKVNVPKIPTNQNVSPSQRDEVIQWLAKFKYQFNLYPETFALA

Parental  SSLLDRFLATVKAHPKYLNCIAISCFFLAAKTVEEDEKIPVLKVLARDSFCGCSSSEILRMERIILDKLN
          SSLLDR.LATVKAHPKYLN.IAIS.FFLAAKTVEEDEKIPVLKVLARDSFCGCSSSEILRMERIILDKLN
Retrocopy SSLLDRILATVKAHPKYLNYIAISWFFLAAKTVEEDEKIPVLKVLARDSFCGCSSSEILRMERIILDKLN

Parental  WDLHTATPLDFLHIFHAIAVSARPQLLFSLPKLSPSQHLAVLTKQLLHCMACNQLLQFKGSMLALAMVSL
          WDLH.ATPLDFLHIFHAI.VS.RPQLLFS.PKLSPSQHL..LTK.LL.CMACNQLLQFKGSMLALAMVSL
Retrocopy WDLHMATPLDFLHIFHAIVVSTRPQLLFSWPKLSPSQHLVILTKKLLPCMACNQLLQFKGSMLALAMVSL

Parental  EMEKLIPDWLPLTIELLQKAQMDSSQLIHCR-ELVAYHLSALQSALPLNSVYVYRPLKHTLVTCDKGAFK
          EMEK.IPDWLPLTIELLQ.A.M.SSQ.IHCR.ELVAYH.SA.QSALPLNSVYVYRPLKHTLVTCDKGAF.
Retrocopy EMEKPIPDWLPLTIELLQEAEMGSSQ*IHCR>ELVAYHCSAPQSALPLNSVYVYRPLKHTLVTCDKGAFT

Parental  LHPSSVSGPDFSKDNSKPEVPVRGPAAFHLHLPAASGCKQTSAKRKVEEMEVDDFYDGIKRLYNEDNGPE
          LHPSSVSGPDFSKD.SKPEVPVRGPAAFHLHLPAASGCKQTSAK.KVEEMEVDDF..GIK.LYNEDNGPE
Retrocopy LHPSSVSGPDFSKDKSKPEVPVRGPAAFHLHLPAASGCKQTSAKWKVEEMEVDDFSNGIKPLYNEDNGPE

Parental  NVGSVCGTDLSRQEGHASPCPPLQPVSVM
          NVGSVCGTDLSRQEGHASPCPPLQPVSVM
Retrocopy NVGSVCGTDLSRQEGHASPCPPLQPVSVM

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	0.05 RPM	150.36 RPM
SRP007412_cerebellum	0.00 RPM	150.41 RPM
SRP007412_heart	0.06 RPM	76.42 RPM
SRP007412_kidney	0.12 RPM	174.31 RPM
SRP007412_liver	0.00 RPM	83.07 RPM
SRP007412_testis	1.28 RPM	161.18 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2730 was not detected

EST

No EST(s) were mapped for retro_mmus_2730 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_122524	1064 libraries	4 libraries	2 libraries	2 libraries	0 libraries
TSS #2	TSS_122525	1056 libraries	9 libraries	4 libraries	0 libraries	3 libraries

The graphical summary, for retro_mmus_2730 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_2730 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2730 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014768	1 retrocopy	retro_cjac_1311,
Echinops telfairi	ENSETEG00000000952	1 retrocopy	retro_etel_1137,
Loxodonta africana	ENSLAFG00000029218	1 retrocopy	retro_lafr_295,
Macaca mulatta	ENSMMUG00000019904	1 retrocopy	retro_mmul_2529,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Mus musculus	ENSMUSG00000063015	2 retrocopies	retro_mmus_1211, retro_mmus_2730 ,
Tarsius syrichta	ENSTSYG00000009907	1 retrocopy	retro_tsyr_834,
Vicugna pacos	ENSVPAG00000011865	1 retrocopy	retro_vpac_197,