RetrogeneDB ID: retro_itri_772

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393320.1:7496027..7496852(-)
• Located in intron of: ENSSTOG00000001289

Retrocopy information

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

Parental gene information

• Parental gene symbol: AURKA
• Ensembl ID: ENSSTOG00000011958
• Aliases: None
• Description: aurora kinase A [Source:HGNC Symbol;Acc:11393]

Sequence

>retro_itri_772
AACTTATTTTCCTTTCCAACATAGGCTACAGTTCCATTGGGTGATAGTCCAAAACATGTTCTGGGACTTAGCACATTCCT
TCTCAGACTGCTTCTGTAAGAAGTGGCCAGACTCAGTGAATCCATGTTCTTTAAATTCTTCCCAGCATATTTCTTTTTAA
GAACAAAAAGTTTGTCTCCTGTCAGAAACTAGCAACAGAAGCAATTGCAGGCAACTAGTGTACTTTAGCCTGTCATCCTG
TGAACAATATCCAGAAAAATGAGCAGCCTCAGCCATAAGCACCTGGAAATAATCCTGAAAAGGAACTGGCAACAAAACAT
AAAAGTTAAGACTCAAAAGAAAAGGCAGTGGGCTTTGGAAGATTTGACACTGCTCCCCCACTGGGTAAAGGAGATTTTGG
TAATGTTTATTTGAGAAGAGGAAAACAAAGCAAGTTTATCCTGGCTCCTAAATTGTTTAAAGTTCAGCTGGAGAATGCAT
GAGTAGAGCATTATATCAGGATAAAAGTAGAAATCCAGTCCCACCATAGGCATTCTAATATTCTCAAGCTGTAAGATTAT
TTCATGATGTTACCAGAGTCTACCTAATTCTAGAATATGTACCACTTGAAACAGTCTAAAGAGAAATTCTGAAACTTTCC
AAGTTTGAGGAGCAGAGAATTGCTACTTAGGTTGCTAAACTGCAAATGTTCTGTCTTACTACTATTTAAAGATAGCTATT
CATAGAGACATTATGCCAGAGAACAAGCTACTTGGATCAGCTGGAGAGCTTAAAATCACCAATTCTGAGCGATCAGTACA
CGCTCCAATCTCCAAGAGAACCACT

Alignment

ORF - retro_itri_772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.84 %
• Parental protein coverage: 70.28 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  NCVSGPVKATVPHGEGPKRVLV-TQHIPSQNPLSTSSGQAQRIL-CPSNSSQRVPLHAQKL-VSSQKLGQ
          N..S.P..ATVP.G..PK.VL..T.HIPSQ...S..SGQ.Q.I..C..NSSQ......QK..VS.QKL..
Retrocopy NLFSFPT*ATVPLGDSPKHVLG<T*HIPSQTA-SVRSGQTQ*IH<CSLNSSQHISF*EQKV>VSCQKLAT

Parental  KQLQAASIPRPVSRPVNNTQKSEQSQPSGPGNNPERELASKQKNEDSK-KRQWTLED-FDIGRPLGKGKF
          ....A.........PVNN.QK.EQ.QP..PGNNPE.ELA.K.K..DSK.KRQW.LED.FD...PLGKG.F
Retrocopy EAI-AGN*CTLACHPVNNIQKNEQPQP*APGNNPEKELATKHKS*DSK>KRQWALED<FDTAPPLGKGDF

Parental  GNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGY-FHDATRVYLILEYA
          GNVYL.R.KQSKFILA.K.LFK.QLE.A.VEH..R..VEIQSH.RH.NIL.L..Y.FHD.TRVYLILEY.
Retrocopy GNVYLRRGKQSKFILAPK-LFKVQLENA*VEHYIRIKVEIQSHHRHSNILKL*DY<FHDVTRVYLILEYV

Parental  PLGTVYRELQKLSKFDEQRTATYITEL-ANALSYCHSKRVIHRDIKPENLLLGSTGELKIADFGWSVHAP
          PL.TV.RE..KLSKF.EQR.AT....L.AN.LSY...K..IHRDI.PEN.LLGS.GELKI.....SVHAP
Retrocopy PLETV*REILKLSKFEEQRIAT*VAKL<ANVLSYYYLKIAIHRDIMPENKLLGSAGELKITNSERSVHAP

Parental  SSRYVT
          .S...T
Retrocopy ISKRTT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_772 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_772 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 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,
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,