RetrogeneDB ID: retro_mmus_1211

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:56865412..56866355(+)
• Located in intron of: None

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_1211
ATGAAGTTTCCAGGACCTTTGGAAAACCAGAGATTGTCTTCTCTGTTGGAAAGGGCAATCTCCAGGGAAGCCCAGATGTG
GAAGGTGAATGTGCCGAAAATACCTACAAATCAGAATGTTTCTCCATCCCAGAGAGATGAAGTAATTCAATGGTTGGCCA
AACTCAAATACCAGTTCAACCTCTATCCAGAAACATTTGCTCTATCAAGCAGTCTTTTGGATAGGTTTTTAGCTACAGTA
AAAGCCCATCCAAAATATTTGAATTGTATTGCAATCAGCTGTTTTTTTTTTCTGGCTGCTAAGACTGTTGAGGAAGATGA
GAAAATTCCAGTGCTAAAGGTATTGGCAAGAGACAGTTTCTGTGGATGTTCCTCATCTGAGATTTTGAGAATGGAGAGAA
TTATTCTGGATAAATTGAATTGGGATCTTCACACGGCCACACCATTGGATTTTCTTCACATTTTTCATGCCATTTCGGTG
TCAACTAGGCCTCAGTTACTTTTCAGTTTGCCCAAATTGAGCCCATCTCAACATTTGGCAGTCCTGACTAAGCAGCATGC
TTCACTGTATGGACTGCAACCAACTTCTGCAGTTCAAAGGGTCCATGCTGGCTCTGGCCATGGTTAGTCTGGAAATGGAG
AAACTCATTCCTGATTGGCTTCCTCTTAAGATTGAACTGCGTCAGGGAGCACAGATGGGCAGCTCCCAGTTGATCCACTG
TCGGGAGCTGGTGGCATATCACCGTTCTGCTCTGCAGTCTGCCCTGCCTCTAAATTCCGTTTTTGTCTACCGTCCCCTCA
AGCACACCCTGGTAACCTGTGACAAAGGAGCACTCAAATTACATCCCTCCTCTGTCTCAGGCCCAGATTTCTCCAAGGAC
AACAGCAAGTCAGAAGTACCAGTCCGAGGTCCAGCAGCCTTCCACCTGCATCTCCCCGCAGCC

Alignment

ORF - retro_mmus_1211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.29 %
• Parental protein coverage: 83.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKFPGPLENQRLSSLLERAISREAQMWKVNVPKIPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALAS
          MKFPGPLENQRLSSLLERAISREAQMWKVNVPKIPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFAL.S
Retrocopy MKFPGPLENQRLSSLLERAISREAQMWKVNVPKIPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALSS

Parental  SLLDRFLATVKAHPKYLNCIAISCFF-LAAKTVEEDEKIPVLKVLARDSFCGCSSSEILRMERIILDKLN
          SLLDRFLATVKAHPKYLNCIAIS....LAAKTVEEDEKIPVLKVLARDSFCGCSSSEILRMERIILDKLN
Retrocopy SLLDRFLATVKAHPKYLNCIAISXXXXLAAKTVEEDEKIPVLKVLARDSFCGCSSSEILRMERIILDKLN

Parental  WDLHTATPLDFLHIFHAIAVSARPQLLFSLPKLSPSQHLAVLTKQ-LLHCMACNQLLQFKGSMLALAMVS
          WDLHTATPLDFLHIFHAI.VS.RPQLLFSLPKLSPSQHLAVLTKQ..LHCM.CNQLLQFKGSMLALAMVS
Retrocopy WDLHTATPLDFLHIFHAISVSTRPQLLFSLPKLSPSQHLAVLTKQ>MLHCMDCNQLLQFKGSMLALAMVS

Parental  LEMEKLIPDWLPLTIELLQKAQMDSSQLIHCRELVAYHLSALQSALPLNSVYVYRPLKHTLVTCDKGAFK
          LEMEKLIPDWLPL.IEL.Q.AQM.SSQLIHCRELVAYH.SALQSALPLNSV.VYRPLKHTLVTCDKGA.K
Retrocopy LEMEKLIPDWLPLKIELRQGAQMGSSQLIHCRELVAYHRSALQSALPLNSVFVYRPLKHTLVTCDKGALK

Parental  LHPSSVSGPDFSKDNSKPEVPVRGPAAFHLHLPAA
          LHPSSVSGPDFSKDNSK.EVPVRGPAAFHLHLPAA
Retrocopy LHPSSVSGPDFSKDNSKSEVPVRGPAAFHLHLPAA

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	0.54 RPM	150.36 RPM
SRP007412_cerebellum	0.39 RPM	150.41 RPM
SRP007412_heart	0.25 RPM	76.42 RPM
SRP007412_kidney	0.87 RPM	174.31 RPM
SRP007412_liver	0.16 RPM	83.07 RPM
SRP007412_testis	0.55 RPM	161.18 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1211 was not detected

EST

No EST(s) were mapped for retro_mmus_1211 retrocopy.

TSS

No TSS is located nearby retro_mmus_1211 retrocopy 5' end.

Lab

retro_mmus_1211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1211 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,