RetrogeneDB ID: retro_pabe_231

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:29455372..29456356(+)
• Located in intron of: ENSPPYG00000000207

Retrocopy information

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

Parental gene information

• Parental gene symbol: AURKA
• Ensembl ID: ENSPPYG00000011148
• Aliases: None
• Description: aurora kinase A [Source:HGNC Symbol;Acc:11393]

Sequence

>retro_pabe_231
CCAGTTGGAGGTCCAAAACGTGTTCTCGTGACTCAGCAATTTCCTTGTCAGAATCCATTACCTGCAAATAGTGGCCAGGC
TCAGTGGGTCTTATGTCCTTCAAATTCTTCCCAGCGTGTTCCTTTGCAAGCACAAAAGCTTGTCTCCAGTCACAAGCCAG
TTCAGAATCAGAAGCAGAAGCAAGTACAGGCAACCAGTGTACCTCATCCTGCCTCCAGGCCACTGAATAACACCCAAAAG
AGCAAGCAGTCCCTGCTGTCGGCACCTGAAAATAATCCTGAGGAGGAACTGGCATCAAAACAGAAAAATGAAGAATCAAA
AAAGAGGCAATGGGCTTTGGAAGACCTTGAAATTGGTCTCCCTCTGGGTAAAGGAAAGTTTAGTAATGTTTATTTGGCAA
GAGAAAAACAAAGCAAGTTTATTCTGGCTCTTAAAGTGTTATTTAAAGCTCAGCTGGAGAAAGCAGGAGTGGAGCATCAA
CTCAGAAGAGAAGTAGAAATACAGTCCCACCTTCAACATCCTAATATAATCAGACTGTATGGTTATTTCCATGATGCCAC
CAGAGTCTACCTAATTCTGGAATGTACACCACTTGAAACAGTCAATAGAGAACTTCAGAAACTTTCAAAGTTTGATGAGC
AGAGAACTGCTACTTATATCACAGAATTGGCAAATGCCGTGTCTTACTGTCATTCAAAGACAGTTATTCATAGAGACATT
AAGCCAGAGAACTTACTTCTTGGATCAGCTGGAGAGCTTGAAATTGTAAATTTTGGGTGGTCAGTACATGTTCCATCTTC
CAGGAGGACCACTCTCTGTGGCATCCTGGACTACCTGCCCCCCGAAATGATTGAAGGTCGGATGCATGATGAGAAGGTGG
ATCTCTGGAGCCTTGGAGTTCTTTGCTGTGAATTTTTAGTTGAGAAGCCTCCTTTTGAGGCAAATACATACCAGGAGACC
TACAAAAGAATATCACAGGTTGAG

Alignment

ORF - retro_pabe_231 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.4 %
• Parental protein coverage: 81.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVGGPKRVLVTQQFPCQNPLPANSGQAQRVLCPSNSSQRVPLQAQKLVSSHKPVQNQKQQKQLQATSVPH
          PVGGPKRVLVTQQFPCQNPLPANSGQAQ.VLCPSNSSQRVPLQAQKLVSSHKPVQNQKQ.KQ.QATSVPH
Retrocopy PVGGPKRVLVTQQFPCQNPLPANSGQAQWVLCPSNSSQRVPLQAQKLVSSHKPVQNQKQ-KQVQATSVPH

Parental  PVSRPLNNTQKSKQPLPSAPENNPEEELASKQKNEESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSK
          P.SRPLNNTQKSKQ.L.SAPENNPEEELASKQKNEESKKRQWALED.EIG.PLGKGKF.NVYLAREKQSK
Retrocopy PASRPLNNTQKSKQSLLSAPENNPEEELASKQKNEESKKRQWALEDLEIGLPLGKGKFSNVYLAREKQSK

Parental  FILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLS
          FILALKVLFKAQLEKAGVEHQLRREVEIQSHL.HPNI.RLYGYFHDATRVYLILE..PL.TV.RELQKLS
Retrocopy FILALKVLFKAQLEKAGVEHQLRREVEIQSHLQHPNIIRLYGYFHDATRVYLILECTPLETVNRELQKLS

Parental  KFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLCGTLDYL
          KFDEQRTATYITELANA.SYCHSK.VIHRDIKPENLLLGSAGEL.I..FGWSVH.PSSRRTTLCG.LDYL
Retrocopy KFDEQRTATYITELANAVSYCHSKTVIHRDIKPENLLLGSAGELEIVNFGWSVHVPSSRRTTLCGILDYL

Parental  PPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVE
          PPEMIEGRMHDEKVDLWSLGVLC.EFLV.KPPFEANTYQETYKRIS.VE
Retrocopy PPEMIEGRMHDEKVDLWSLGVLCCEFLVEKPPFEANTYQETYKRISQVE

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
SRP007412_brain_prefrontal_cortex	0.06 RPM	0.66 RPM
SRP007412_cerebellum	0.00 RPM	3.04 RPM
SRP007412_heart	0.18 RPM	0.90 RPM
SRP007412_kidney	0.03 RPM	0.60 RPM
SRP007412_liver	0.24 RPM	0.89 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_231 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_231 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_231 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_510
Pan troglodytes	retro_ptro_381
Gorilla gorilla	retro_ggor_470
Macaca mulatta	retro_mmul_431

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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,