RetrogeneDB ID: retro_mmus_2455

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:44752300..44753146(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080916
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Aurkc
• Ensembl ID: ENSMUSG00000070837
• Aliases: Aurkc, AIE1, AIK3, ARK-3, IAK3, Stk13
• Description: aurora kinase C [Source:MGI Symbol;Acc:MGI:1321119]

Sequence

>retro_mmus_2455
CTTTCCTTAGCTACTGGCCAGATGGAGCCCAGCACCTCAACCAGGAAGCATTTCACCATCAATGACTTTGAAATCGGGCG
TCCTCTGGGCAGGGGGAAATTTGGGCGTGTGTACTTGGCTCGGCTCAAGGAAAATCATTTCATCGTGGCCCTGAAGGTCC
TCTTCAAGTCTGAGATAGAGAAGGAGGGATTGGAGCACCAACTTCGCAGGGAAGTGGAGATCCAGGCACACCTACAACAC
CGGAACATCCTTCGCCTGTACAACTACTTCTATGATGACACTCGGATATACTTAATTCTGGAGTATGCTCCAGGAGGAGA
GCTCTATAAGGAGCTTCAGAGACATCAGAAGTTGGACCAGCAGCGTACAGCCACGATAATACAGGAGTTGTCAGATGCCC
TGACCTACTGCCATGAGAAGAAGGTGATTCACAGGGACATCAAGCCAGAGAATCTCCTGCTGGGCCTCAATGGTGAGGTG
AAGATCTCAGACTTTGGGTGGTCTGTGCATACCCCCTCTCTCAGGAGAAAGACAATGTGTGGGACTCTGGACTACTTGCC
CCCGGAAATGATAGCGCAGAAACCGTACAATGAGATGGTTGATCTGTGGTGCATTGGGGTGCTCTGCTATGAGCTGCTGG
TGGGGAAGCCACCCTTTGAGAGCAGCACCTCCAGTGAGACATACAGACGCATCCGCCAGGTGGATTTTAAGTTTCCTTCA
TCAGTGCCTGCAGGAGCCCAGGACTTGATCTCCAAGCTTCTTAGGTACCATCCTTCAGAGCGGCTGAGCCTGGCCCAAGT
CCTGAAGCACCCCTGGGTCAGGGAACACTCTCGAAGGGTGCTGCCT

Alignment

ORF - retro_mmus_2455 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.65 %
• Parental protein coverage: 89.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSLATGQMEPSTSTRKHFTINDFEIGRPLGRGKFGRVYLARLKENHFIVALKVLFKSEIEKEGLEHQLRR
          .SLATGQMEPSTSTRKHFTINDFEIGRPLGRGKFGRVYLARLKENHFIVALKVLFKSEIEKEGLEHQLRR
Retrocopy LSLATGQMEPSTSTRKHFTINDFEIGRPLGRGKFGRVYLARLKENHFIVALKVLFKSEIEKEGLEHQLRR

Parental  EVEIQAHLQHRNILRLYNYFYDDTRIYLILEYAPGGELYKELQRHQKLDQQRTATIIQELSDALTYCHEK
          EVEIQAHLQHRNILRLYNYFYDDTRIYLILEYAPGGELYKELQRHQKLDQQRTATIIQELSDALTYCHEK
Retrocopy EVEIQAHLQHRNILRLYNYFYDDTRIYLILEYAPGGELYKELQRHQKLDQQRTATIIQELSDALTYCHEK

Parental  KVIHRDIKPENLLLGLNGEVKISDFGWSVHTPSLRRKTMCGTLDYLPPEMIAQKPYNEMVDLWCIGVLCY
          KVIHRDIKPENLLLGLNGEVKISDFGWSVHTPSLRRKTMCGTLDYLPPEMIAQKPYNEMVDLWCIGVLCY
Retrocopy KVIHRDIKPENLLLGLNGEVKISDFGWSVHTPSLRRKTMCGTLDYLPPEMIAQKPYNEMVDLWCIGVLCY

Parental  ELLVGKPPFESSTSSETYRRIRQVDFKFPSSVPAGAQDLISKLLRYHPSERLSLAQVLKHPWVREHSRRV
          ELLVGKPPFESSTSSETYRRIRQVDFKFPSSVPAGAQDLISKLLRYHPSERLSLAQVLKHPWVREHSRRV
Retrocopy ELLVGKPPFESSTSSETYRRIRQVDFKFPSSVPAGAQDLISKLLRYHPSERLSLAQVLKHPWVREHSRRV

Parental  LP
          LP
Retrocopy LP

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	0.07 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.96 RPM	5.81 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2455 was not detected

EST

No EST(s) were mapped for retro_mmus_2455 retrocopy.

TSS

No TSS is located nearby retro_mmus_2455 retrocopy 5' end.

Lab

retro_mmus_2455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2455 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023297	1 retrocopy	retro_cfam_1177,
Echinops telfairi	ENSETEG00000015413	1 retrocopy	retro_etel_1828,
Macropus eugenii	ENSMEUG00000014431	2 retrocopies	retro_meug_741, retro_meug_947,
Mus musculus	ENSMUSG00000027496	1 retrocopy	retro_mmus_2825,
Mus musculus	ENSMUSG00000070837	1 retrocopy	retro_mmus_2455 ,
Otolemur garnettii	ENSOGAG00000000999	6 retrocopies	retro_ogar_1122, retro_ogar_1159, retro_ogar_1240, retro_ogar_1293, retro_ogar_2384, retro_ogar_923,