RetrogeneDB ID: retro_cfam_1027

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:4441767..4442991(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004073
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AURKA
• Ensembl ID: ENSCAFG00000029331
• Aliases: None
• Description: aurora kinase A [Source:HGNC Symbol;Acc:11393]

Sequence

>retro_cfam_1027
GGCATTATGGACAAATCTAAAGAAAACTGCATTGCAGGGCCTGTTAAGACTACAATTGCACTTGGTGATGGTCCAAAACG
TGTTCTGGTGACTCAGCAAGTTCCTTCACAGAATCCGTTATCTGCAAATAGTGGCCAGGCCCAGCAGGTCTTGTGTCCTT
CAAATTCTTCCCAGCGAGTTCCTCCACAAACCCAAAAGCTCGTCTCCAGCCATAAACCAGCTCAGAATCTGAAGCAGAAG
CAATTGCAGGCAACTGGTGTCCCTTGTCCTGCCTCTAGGTCACTGAATAGTACCCAAAAGAGTGAGCAACCCTCGTCATC
AGCCCCTGGAAATAATTCTGAAAAGGAACTGGCAACAAAACAGAAAAATGAAGAATCAAAAAAAAAAAAGGCAATGGGCT
TTGGAAGATTTTGAAATTGGTCGCCCACTGGGTAAAGGAAAGTTTGGTAATGTTTACTTGGCAAGGGAAAAACAAAGCAA
GTTTATCCTGGCTATTAAAGTATTATTTAAAGCTCAACTGGAGAAAGCAGGAGTTGACCATCAGCTGAGAAGAGAAGTAG
AAATACAGTCCCACCTTAGGCATCCAAATATTCATAGGCTGTATGGTTATTTCCATGATGCCACCAGAGTTTACCTAATT
CTAGAATATGCACCTTTTGGAGCTGTCTACAGAGAACTTCAGAAACTGTCAAAGTTTGATGAACAGAGAACTGCTACTTA
TATCACAGAGTTGGCAGATGCCCTGTCTTACTGTCACTCAAAGAGAGTCATTCACAGAGACATTAAGCCAGAGAACCTAC
TCCTTGAATCAGCTGGAGAGCTTAAGATTGCAGATTTTGGGTGGTCAGTACATGCTCCATCCTCCAGGAGAACCACCCTG
TGTGGCACCCTGGATTACTTGCCCCCAGAGATGATTGAAGGCCGAATGCGTGATGAGAAGGTGGATCTCTGGAGCCTTGG
GGTTCTTTGCTATGAATTTCTAGTTGGGAAGCCTCCTTTTGAGGTAAGCACATACCAAGAGACCTACAAAAGAATATCAT
GGGTTGAATTCACATTCCCTGACTTCGGGCCGGAGGGAGCCAGGGATCTCATTCAAGACTGTTGAAACATAATCCCAGCC
AAAGGCCAACTCTCAAGGATGTACTTGAACACCCGTGGATCATGGCTAGCTCATCAAAACCATCAAGTAGCCAAAAAAGC
AAAGACTCAACTAGCAAACAGTCT

Alignment

ORF - retro_cfam_1027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.73 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GIMDKSKENCIAGPVKTAIALGDGPKRVLVTQQVPSQNPLSANSGQAQRVLCPSNSSQRVPPQTQKLVSS
          GIMDKSKENCIAGPVKT.IALGDGPKRVLVTQQVPSQNPLSANSGQAQ.VLCPSNSSQRVPPQTQKLVSS
Retrocopy GIMDKSKENCIAGPVKTTIALGDGPKRVLVTQQVPSQNPLSANSGQAQQVLCPSNSSQRVPPQTQKLVSS

Parental  HKPAQNLKQKQLQATGVPRPASRSLNNTQKSEQPS-SSAPGNNSEKELATKQKNEESKKR-QWALEDFEI
          HKPAQNLKQKQLQATGVP.PASRSLN.TQKSEQPS.S....N............E......QWALEDFEI
Retrocopy HKPAQNLKQKQLQATGVPCPASRSLNSTQKSEQPSSSAPGNNSEKELATKQKNEEXXXXX>QWALEDFEI

Parental  GRPLGKGKFGNVYLAREKQSKFILAIKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATR
          GRPLGKGKFGNVYLAREKQSKFILAIKVLFKAQLEKAGV.HQLRREVEIQSHLRHPNI.RLYGYFHDATR
Retrocopy GRPLGKGKFGNVYLAREKQSKFILAIKVLFKAQLEKAGVDHQLRREVEIQSHLRHPNIHRLYGYFHDATR

Parental  VYLILEYAPLGAVYRELQKLSKFDEQRTATYITELADALSYCHSKRVIHRDIKPENLLLGSAGELKIADF
          VYLILEYAP.GAVYRELQKLSKFDEQRTATYITELADALSYCHSKRVIHRDIKPENLLL.SAGELKIADF
Retrocopy VYLILEYAPFGAVYRELQKLSKFDEQRTATYITELADALSYCHSKRVIHRDIKPENLLLESAGELKIADF

Parental  GWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEASTYQETYKRISRVE
          GWSVHAPSSRRTTLCGTLDYLPPEMIEGRM.DEKVDLWSLGVLCYEFLVGKPPFE.STYQETYKRIS.VE
Retrocopy GWSVHAPSSRRTTLCGTLDYLPPEMIEGRMRDEKVDLWSLGVLCYEFLVGKPPFEVSTYQETYKRISWVE

Parental  FTFPDFVPEGARDLI-SRLLKHNPSQRPTLKDVLEHPWIMANSSKPSSSQKNKDSTSKQS
          FTFPDF.PEGARDLI.SRLLKHNPSQRPTLKDVLEHPWIMA.SSKPSSSQK.KDSTSKQS
Retrocopy FTFPDFGPEGARDLI<SRLLKHNPSQRPTLKDVLEHPWIMASSSKPSSSQKSKDSTSKQS

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
SRP012049_cerebellum	0.04 RPM	4.79 RPM
SRP017611_brain	0.08 RPM	1.98 RPM
SRP017611_kidney	0.00 RPM	1.85 RPM
SRP017611_liver	0.07 RPM	1.09 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1027 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1027 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	ENSCAFG00000023297	1 retrocopy	retro_cfam_1177,
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,