RetrogeneDB ID: retro_rnor_670

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:11229637..11230558(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aurka
• Ensembl ID: ENSRNOG00000004479
• Aliases: Aurka, ARK-1, Stk6
• Description: aurora kinase A [Source:RefSeq peptide;Acc:NP_695208]

Sequence

>retro_rnor_670
GTCTCCAGGCCTGTTAAGACCACAGTTCCCTTCGGTCCGAAACGAGTCTTGGTGACTGAGCAGATTCCTTCTCAGCACCC
AGGATCAGCGAGCAGTGGCCAGGCCCAGTGGGTCCTGTGTCCTTCCAACTCCCAGCGTGTCCCTCCACAAGCACAGAAAC
CTGTCGCAGGTCAGAAGTCAGTGCTAAAGCAGTTGCCAGCTGCCAGCGTTCCTCGACCTGTGTCCCGGCTAAGTAACCCC
CCAGAAGAGTGAGCAGCCACAGCCTGCAGCCTCGGGAAATTCTGAAAAGGAACAGACATCCATCCAGAAAACTGAAGACT
CAAAAAGAAGGGAGTGGACTTTGGAAGATTTTGACATTGGCCGCCCACTAGGAAAAGGGAAGTTTGGAAATGTCTATTTG
GCGAGGGAGAAGCAAAGCAAGTTCATCCTGGCTCTGAAGATGCTGTTTAAAGTACAGCTGGAGAAGCAGGTGTGGAGCAC
CAGCTTCGGAGAGAAGTGGAGATCCAGTCCCACCTGCGGCACCCCAACATCCTCGGGTTGTATGGGTATTCCCATGACGC
CACCAGAGTTTATCTAATTCTAGAATATGCGCCCCTTGGAACAGTGTATAGAGAGCTTCAAAAACTCTCCAAGTTTGACG
AGCAGAGAATAGCTACCTACATCACGGAGTTGGCGAATGCTTTGTCCTAGTGCCATTCAAAGAGAGTCATCCACAGAGAC
ATCAAGCCAGAGAACCCGCTGCTTGGCTCAAATGGGGAGTTGAAGCTCGCAGACTTCGGGTGGTCTGCGCATGCTCCATC
TTCCAGGAGACCCACGCTGTACTGCACCGTGGACTACCTGCCCCCGGAGATGATTGAAGGGCAGATGCATGATGAGGAGG
TGGATCTCTGGAGCCTGGGTGTGCTCTGCTATGAATTCCTA

Alignment

ORF - retro_rnor_670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.26 %
• Parental protein coverage: 77.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSRPVKSTVPFGPKRVLVTEQIPSQHPGSASSGQAQRVLCPSNSQRVPPQAQKPVAGQKPVLKQLPAASG
          VSRPVK.TVPFGPKRVLVTEQIPSQHPGSASSGQAQ.VLCPSNSQRVPPQAQKPVAGQK.VLKQLPAAS.
Retrocopy VSRPVKTTVPFGPKRVLVTEQIPSQHPGSASSGQAQWVLCPSNSQRVPPQAQKPVAGQKSVLKQLPAASV

Parental  PRPASRLSNP-QKSEQPQPAASGNNSEKEQTSIQKTEDSKKRQWTLEDFDIGRPLGKGKFGNVYLAREKQ
          PRP.SRLSNP.QKSEQPQPAASGN.SEKEQTSIQKTEDSK.R.WTLEDFDIGRPLGKGKFGNVYLAREKQ
Retrocopy PRPVSRLSNP>QKSEQPQPAASGN-SEKEQTSIQKTEDSKRREWTLEDFDIGRPLGKGKFGNVYLAREKQ

Parental  SKFILALKVLFKVQLEK-AGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQ
          SKFILALK.LFKVQLEK.AGVEHQLRREVEIQSHLRHPNIL.LYGY.HDATRVYLILEYAPLGTVYRELQ
Retrocopy SKFILALKMLFKVQLEK<AGVEHQLRREVEIQSHLRHPNILGLYGYSHDATRVYLILEYAPLGTVYRELQ

Parental  KLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSNGELKIADFGWSVHAPSSRRTTLCGTL
          KLSKFDEQR.ATYITELANALS.CHSKRVIHRDIKPEN.LLGSNGELK.ADFGWS.HAPSSRR.TL..T.
Retrocopy KLSKFDEQRIATYITELANALS*CHSKRVIHRDIKPENPLLGSNGELKLADFGWSAHAPSSRRPTLYCTV

Parental  DYLPPEMIEGRMHDEKVDLWSLGVLCYEFL
          DYLPPEMIEG.MHDE.VDLWSLGVLCYEFL
Retrocopy DYLPPEMIEGQMHDEEVDLWSLGVLCYEFL

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
SRP017611_brain	1.15 RPM	4.03 RPM
SRP017611_kidney	0.91 RPM	3.07 RPM
SRP017611_liver	0.13 RPM	5.24 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_670 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF560471	11229919	11230058	100	139	0	139

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_670 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_670 has 0 orthologous retrocopies within eutheria group .

---

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,