RetrogeneDB ID: retro_mmus_2825

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:50746684..50747412(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aurka
• Ensembl ID: ENSMUSG00000027496
• Aliases: Aurka, AIRK1, ARK-1, AU019385, AW539821, Ark1, Aurora-A, Ayk1, IAK, IAK1, Stk6
• Description: aurora kinase A [Source:MGI Symbol;Acc:MGI:894678]

Sequence

>retro_mmus_2825
CTGACAAGGAAAATACAAAGCAAGTTCATCTTGGCTCTGAAGGTGCTGTTTAAAACGCTGCTGGAGAAGGCAGGTGTGGA
GAACCAGCTATGAAGGGAAGTGGTGATCCAGTCCCACCTTGGGCACCCCAACATCCTCAGGCTTTATGGGTATTTCCATG
ATGTCACCAGAGTTTATCTAATTCTAGAATATGTGTCCCTTGGAACAGTCTATAAAGCACTTCAAAAAAATCTCCAAGTT
GACAAGCAGGGAACAGCTACTTACTGAGTTGGCAAATGCTCTGTCTTACCGTCAAAGAGAATCATCCACAGAGACATTAG
GCCAGAGACCTGCTTCTTGGGTCAAACAGAGAGTTGAAGATCTCAGACTTCGGACGGTCTGTACAAGCTCCATCTTCCAG
GAGAACCACACTGTGGCACCCTGGACTACCTGCCCCGGAGATGATTGAAGGCCGGATGCATGATGAGAAGGTGGACCTCT
GGAGCCTCGGTGTTCTCTGCTATGAGTTCCTAGCAGGGATGCCTCACTCGGAGACACACACTTACCAGGAGACCCACAGA
AGGATATCATGGCTTGAATCCAAATTCCCTGATGCTGTGATGGGAGCCGGTGACCTCATTTCAAGACTGTAAAAAATACA
ACTCAGGCCGAAGGCAGAAGTCCTTGAGCACCCTTGGATCACAGCTAATTCCTCAAAATCTCCAACTGGCCACAAAAGCA
AAGAGCCA

Alignment

ORF - retro_mmus_2825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.47 %
• Parental protein coverage: 60.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LARERQSKFILALKVLFKTQLEKANVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTV
          L.R..QSKFILALKVLFKT.LEKA.VE.QL.REV.IQSHL.HPNILRLYGYFHD.TRVYLILEY..LGTV
Retrocopy LTRKIQSKFILALKVLFKTLLEKAGVENQL*REVVIQSHLGHPNILRLYGYFHDVTRVYLILEYVSLGTV

Parental  YRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPE-NLLLGSNGELKIADFGWSVHAPSSRRT
          Y..LQK....D.Q.TA...T......S...SKR.IHRDI.PE..LLLGSN.ELKI.DFG.SV.APSS.R.
Retrocopy YKALQKNLQVDKQGTA---TY*VGKCSVLPSKRIIHRDIRPE<DLLLGSNRELKISDFGRSVQAPSS-RR

Parental  TM-CGTLDYLP-PEMIEGRMHDEKVDLWSLGVLCYEFLVGMPPFEAHTYQETYRRISRVEFTFPDFVTEG
          T..CGTLDYLP.PEMIEGRMHDEKVDLWSLGVLCYEFL.GMP..E.HTYQET.RRIS..E..FPD.V..G
Retrocopy TT>CGTLDYLP<PEMIEGRMHDEKVDLWSLGVLCYEFLAGMPHSETHTYQETHRRISWLESKFPDAVM-G

Parental  ARDLISRLLKHNASQRLTLAEVLEHPWIKANSSKPPTGHTSKEP
          A.DLISRL.K..........E...HPWI.ANSSK.PTGH.SKEP
Retrocopy AGDLISRL*KIQLRPKAEVLE---HPWITANSSKSPTGHKSKEP

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	1.33 RPM
SRP007412_cerebellum	0.00 RPM	1.00 RPM
SRP007412_heart	0.00 RPM	1.12 RPM
SRP007412_kidney	0.00 RPM	1.21 RPM
SRP007412_liver	0.00 RPM	1.67 RPM
SRP007412_testis	0.00 RPM	116.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2825 was not detected

EST

No EST(s) were mapped for retro_mmus_2825 retrocopy.

TSS

No TSS is located nearby retro_mmus_2825 retrocopy 5' end.

Lab

retro_mmus_2825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2825 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029331	3 retrocopies	retro_cfam_1027, retro_cfam_257, retro_cfam_764,
Choloepus hoffmanni	ENSCHOG00000005976	8 retrocopies	retro_chof_1302, retro_chof_1575, retro_chof_1709, retro_chof_2213, retro_chof_2389, retro_chof_259, retro_chof_565, retro_chof_764,
Cavia porcellus	ENSCPOG00000006633	1 retrocopy	retro_cpor_106,
Felis catus	ENSFCAG00000024493	1 retrocopy	retro_fcat_495,
Homo sapiens	ENSG00000087586	1 retrocopy	retro_hsap_510,
Gorilla gorilla	ENSGGOG00000007197	1 retrocopy	retro_ggor_470,
Myotis lucifugus	ENSMLUG00000007925	1 retrocopy	retro_mluc_1931,
Macaca mulatta	ENSMMUG00000000070	1 retrocopy	retro_mmul_431,
Mus musculus	ENSMUSG00000027496	1 retrocopy	retro_mmus_2825 ,
Mus musculus	ENSMUSG00000070837	1 retrocopy	retro_mmus_2455,
Nomascus leucogenys	ENSNLEG00000007029	1 retrocopy	retro_nleu_1553,
Otolemur garnettii	ENSOGAG00000004441	3 retrocopies	retro_ogar_2805, retro_ogar_3440, retro_ogar_980,
Pongo abelii	ENSPPYG00000011148	1 retrocopy	retro_pabe_231,
Pan troglodytes	ENSPTRG00000013646	1 retrocopy	retro_ptro_381,
Rattus norvegicus	ENSRNOG00000004479	2 retrocopies	retro_rnor_664, retro_rnor_670,
Sus scrofa	ENSSSCG00000007493	1 retrocopy	retro_sscr_936,
Ictidomys tridecemlineatus	ENSSTOG00000011958	2 retrocopies	retro_itri_366, retro_itri_772,
Tupaia belangeri	ENSTBEG00000013284	2 retrocopies	retro_tbel_1137, retro_tbel_2604,
Tarsius syrichta	ENSTSYG00000009221	1 retrocopy	retro_tsyr_378,