RetrogeneDB ID: retro_itri_366

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393286.1:3701446..3702604(-)
• Located in intron of: None

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_366
GTTTCAGGACCCGTTAAAGCTACAGTTCCACATGGTGAAGGTCCAAAACGTGTTCTGGTCACTCAGCATATTCCTTCTCA
GAACCCGTTGTCTACAAGCAGTGGCCAGGCTCAGCGGATCTTATGTCCTTCAAATTCTTCCCAGCGTGTTCCTTTGCACG
CACAAAAGCTCGTCTCCAGTCAGAAACTGGGACAGAATAAATTGCAGGCAGCCAGTATACCTCGTCCTGTCTCCCGGCCA
GTGAACAACACCCAGAAGAGTGAACAATCCCAGCCATCAGTGCCTGGAAATAATCCTGAAAGGGAACTGGCATCAAAACA
GAAAAATGAAGACTTAAAGAAAAGGCAATGGACTTTGGACGATTTTGACACTGGTCGCCCACTGGGTAAAAGAAAGTTTG
GCAATGTTTATTTGGCAAGAGTAAAACAAAGCAAGTTTATTCTGGCTCTTAAAGTGTTATTTAAAGCTCAGCTGGAGAAA
AAAGGAGTGGAGCATCAGCTCAGAAGATAAGTAGAGATCCAGTCCCACCTCCGGCATCCTAATATTCTCAGGCTGTATGG
CTATTTTCATGATGCCACCAGAGTTCACCTAATTCTAGAGTATGCACTGCTTGGAATGGTCTATAGAGAACTTCAGAAAC
TTTCCAAGTTTGATGAGCAGAGAACTGCTACTTACATAACTGAATTAGCAAACGCCCTATCTTACTGCCATTCAAAGAGA
GTTATTCATAGAGACATTAAGCCAGAGAACCTGCTTTTTGGATCAACTGGAGAGCTTAAGATTGCAGATTTTGGGTGGTC
AGTACATGCTCCATCCTCCAGGAGAACCACTCTCTGTGGCACCCTGGACTACCTGCCCCCTGAGATGATTGAAGGCCGGA
TGCATGATGAGAAGGTGGATCTCTGGAGCCTTGGAGTTCTTTGCTATGAATTTCTAGTTGGGCAGCCTCCTTTTGAGGCA
AACACACACCAAGAGACCTACAGAAGAATATCACAGGTTGAATTCACATTCCCTGACTTTGTGACGGAGGGAGCCAGGGA
CCTCATTTCAAGACTGTTGAAGCATAATCCAAGCCAGAGGCCAACTCTAAGTGAAGTACTTGAACACCCCTCGATCACAG
CAAATTCATCAAAGCCACTGAATTGCCAAAAAGGCAGA

Alignment

ORF - retro_itri_366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.2 %
• Parental protein coverage: 96.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSGPVKATVPHGEGPKRVLVTQHIPSQNPLSTSSGQAQRILCPSNSSQRVPLHAQKLVSSQKLGQKQLQA
          VSGPVKATVPHGEGPKRVLVTQHIPSQNPLSTSSGQAQRILCPSNSSQRVPLHAQKLVSSQKLGQ..LQA
Retrocopy VSGPVKATVPHGEGPKRVLVTQHIPSQNPLSTSSGQAQRILCPSNSSQRVPLHAQKLVSSQKLGQNKLQA

Parental  ASIPRPVSRPVNNTQKSEQSQPSGPGNNPERELASKQKNEDSKKRQWTLEDFDIGRPLGKGKFGNVYLAR
          ASIPRPVSRPVNNTQKSEQSQPS.PGNNPERELASKQKNED.KKRQWTL.DFD.GRPLGK.KFGNVYLAR
Retrocopy ASIPRPVSRPVNNTQKSEQSQPSVPGNNPERELASKQKNEDLKKRQWTLDDFDTGRPLGKRKFGNVYLAR

Parental  EKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRE
          .KQSKFILALKVLFKAQLEK.GVEHQLRR.VEIQSHLRHPNILRLYGYFHDATRV.LILEYA.LG.VYRE
Retrocopy VKQSKFILALKVLFKAQLEKKGVEHQLRR*VEIQSHLRHPNILRLYGYFHDATRVHLILEYALLGMVYRE

Parental  LQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSTGELKIADFGWSVHAPSSRYVTLYK
          LQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLL.GSTGELKIADFGWSVHAPSSR..TL..
Retrocopy LQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLFGSTGELKIADFGWSVHAPSSRRTTLCG

Parental  ETRKVPETAVQ-RSTAESTVFWVISVVCH-MLSSCIPVSLNVHLCAHKTPDQVEFTFPDFVTEGARDLIS
          .....P......R...E....W...V.C...L....P...N.H........QVEFTFPDFVTEGARDLIS
Retrocopy TLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGQPPFEANTHQETYRRISQVEFTFPDFVTEGARDLIS

Parental  RLLKHNPSQRPTLSEVLEHPWITANSSKPLNCQKGK
          RLLKHNPSQRPTLSEVLEHP.ITANSSKPLNCQKG.
Retrocopy RLLKHNPSQRPTLSEVLEHPSITANSSKPLNCQKGR

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_366 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_366 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,