RetrogeneDB ID: retro_sscr_936

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:54099635..54100679(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000001776
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AURKA
• Ensembl ID: ENSSSCG00000007493
• Aliases: AURKA, ARK-1, STK6
• Description: Sus scrofa aurora kinase A (AURKA), mRNA. [Source:RefSeq mRNA;Acc:NM_001025225]

Sequence

>retro_sscr_936
ATGGACAAATGTAAAGAAAACTGCATTTCGGGGCTTAAGACTACAATTCCACCGGGTGATGATCCAAAACGCGTTCCAGG
GACCCAGCACTTTCCAGCTCAGAATCCGCCTTCTGCAAACAGCGGCCAGGCTCAGCGGATCTTATGTCCTTCAAATTCCT
CACAGCGCCTTCCTTTGCACGCGCAGAAGCTTGTCTCCAGCCATAAACCAGCTCAGAATCTGAAGCAGAAGCAGTTGCAG
GCAACCAGTGGCCCTCGTCCTGTCTCCAGGCCTCTGAGTAACACCCAGCAGGGTGAGCAGCCCCAGCCGGCAGCGCCTGG
AAATAATCCTGAAAAGGAAGTGGCATCAAGACAGAAAAATGAAGAATCAAAAAAAAGACAATGGGCTTTGGAAGATTTTG
AAGTTGGTTGCCCGCCGGGTAAAGGAAAGTTTGGTAATGTTTATTTAGCAAGAGAAAAACAAAGCAAGTTTATCCTGGCT
CTTAAAATATTGTTTAAAGCTCAGCTGGAGAAGGTAGGAGTTGAACATCATCTGAGAAGAGAAGTAGAAATACAGTCCCA
CCTTAGGCATCCAAATATTCTCAGACTGTATGGTTATTTCCATGACGCTACCAGAGTTTACCTGATCCTGGAATATGTAC
CTCTCGGAGCTGTCTACAGAGAACTTCAGAAACTGTCAAAGTTTGATGAGCAGAGAACTGCTGCTTATATCACAGAGTTG
GCAAATGCCCTGTCTTACTGTCACTCAAAGAGAGATATTAAGCCAGAGAACCTGCTCCTTGGATCCGCTGGAGAGCTTAA
GATTGCCAATTTTGGGTGGTCGGTCCATGCCCCATCCTCCAGGAGAACCACCCTCTGCAGCACCCTGGACTACTTGCCCC
CCGAGATGATCAAAGGCCAGATGCACGACGAGAAGGTGGATCTCTGGAGCCTGGGGGCACTTTGCTATGAATTCCTGGTT
GGGAAGCCCCCCTTTGAGGCAAACACGTACCAAGAGACCTACAAAAGGATATCCCGGGTGGGATTCACCTTCCCTGACTT
TGTT

Alignment

ORF - retro_sscr_936 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.77 %
• Parental protein coverage: 87.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKCKENCISGLKTTVPPGDGPKRVPVTQHFPAQHLPSANSGQAQRVLCPSNSSQRLPSHTQKLVSSHKP
          MDKCKENCISGLKTT.PPGD.PKRVP.TQHFPAQ..PSANSGQAQR.LCPSNSSQRLP.H.QKLVSSHKP
Retrocopy MDKCKENCISGLKTTIPPGDDPKRVPGTQHFPAQNPPSANSGQAQRILCPSNSSQRLPLHAQKLVSSHKP

Parental  VQNLKQKQSQATSGPRPVSRPLSNTQQSEQPQPAAPGNNPEKEAASKQKNEESKKRQWALEDFEIGRPLG
          .QNLKQKQ.QATSGPRPVSRPLSNTQQ.EQPQPAAPGNNPEKE.AS.QKNEE....QWALEDFE.G.P.G
Retrocopy AQNLKQKQLQATSGPRPVSRPLSNTQQGEQPQPAAPGNNPEKEVASRQKNEEXXXXQWALEDFEVGCPPG

Parental  KGKFGNVYLAREKQSKFILALKVLFKTQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLIL
          KGKFGNVYLAREKQSKFILALK.LFK.QLEK.GVEH.LRREVEIQSHLRHPNILRLYGYFHDATRVYLIL
Retrocopy KGKFGNVYLAREKQSKFILALKILFKAQLEKVGVEHHLRREVEIQSHLRHPNILRLYGYFHDATRVYLIL

Parental  EYAPLGAVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVH
          EY.PLGAVYRELQKLSKFDEQRTA.YITELANALSYCHSKR....DIKPENLLLGSAGELKIA.FGWSVH
Retrocopy EYVPLGAVYRELQKLSKFDEQRTAAYITELANALSYCHSKR----DIKPENLLLGSAGELKIANFGWSVH

Parental  APSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPD
          APSSRRTTLC.TLDYLPPEMI.G.MHDEKVDLWSLG.LCYEFLVGKPPFEANTYQETYKRISRV.FTFPD
Retrocopy APSSRRTTLCSTLDYLPPEMIKGQMHDEKVDLWSLGALCYEFLVGKPPFEANTYQETYKRISRVGFTFPD

Parental  FV
          FV
Retrocopy FV

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
SRP014902_placenta	0.00 RPM	3.45 RPM
SRP014902_testis	0.00 RPM	7.36 RPM
SRP018288_heart	0.00 RPM	2.80 RPM
SRP018288_kidney	0.00 RPM	2.66 RPM
SRP018288_liver	0.00 RPM	2.56 RPM
SRP018288_lung	0.00 RPM	12.12 RPM
SRP018856_adipose	0.00 RPM	2.16 RPM
SRP035408_brain	0.00 RPM	4.19 RPM
SRP035408_liver	0.00 RPM	12.86 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_936 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_936 has 0 orthologous retrocopies within eutheria group .

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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,