RetrogeneDB ID: retro_ptro_381

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:199467600..199468632(-)
• Located in intron of: ENSPTRG00000001999

Retrocopy information

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

Parental gene information

• Parental gene symbol: AURKA
• Ensembl ID: ENSPTRG00000013646
• Aliases: None
• Description: Pan troglodytes aurora kinase A (AURKA), mRNA. [Source:RefSeq mRNA;Acc:NM_001246616]

Sequence

>retro_ptro_381
GACCAATCTGAAGAAAACTGCATTTCAGGGCCTGTTGAGGCTAAAACTCCAGCTGGAGGTCCAAAACATGTTCTCGTGAC
TCAGCAATTTCCTTGTCAGAATCCATTACCTGCAAATAGTGGCCAGGCTCAGTGGGTCTTATGTCCTTCAAATTCTTCCC
AGCGTGTTCCTTTGCAAGCACAAAAGCTTGTCTCCAGTCACAAGCCAGTTCAGAATCAGAAGCAGAAGCAATTGCAGGCA
ACCAGTGTACCTCATCCTGCCTCCAGGCCACTGAATAACACCCAAAAGAGCAAGCAGTCCCCGCTGTCGGCACCTGAAAA
TAATCCTGAGGAGGAACTGGCATCAAAACAGAAAAATGAAGAATCAAAAAAGAGGCAATGGGCTTTGGAAGACCTTGAAA
TTGGTCGCCCTCTGGGTAAATGAAAGTTTGGTAATGTTTATTTGGCAAGAGAAAAACAAAGCAAGTTTATTCTGGCTCTT
AAAGTGTTATTTAAAGCTCAGCTGGAGAAAGCAGGAGTGGAGCATCAACTCAGAAGAGAAGTAGAAATACAGTCCCACCT
CCAACATCCTAATATAATCAGACTGTATGGTTATTTCCATGATGCCACCAGAGTCTACCTAATTCTGGAATATACACCAC
TTGAAACAGTCAATACAGAACTTCAGAAACTTTCAAAGTTTGATGAGCAGAGAACTGCTACTTATATCACAGAATTGGCA
AGTGCCCTGTCTTACTGTCATTCAAAACCAGTTATTCATAGAGACATTAAGCCAGAGAACTTACTTCTTGGGTCAGCTGG
AGAGCTTGAAATTGCAAATTTTGGGTGGTCAGAACATGCTCCATCTTCCAGGAGGACCACTCTCTGTGGCACCCTGGACT
ACCTGCCCCCCGAAATGATTGAAGGTCAGATACATGATGAGAAGGTGGATCTCTGGAGCCTTGGAGTTCTTTGCTGTGAA
TTTTTAGTTAGGAAGCCTCCTTTTGAGGCAAATACATACCAAGAGACCTACAAAAGAATATCACGGGTTGAG

Alignment

ORF - retro_ptro_381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 85.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRSKENCISGPVKATAPVGGPKRVLVTQQFPCQNPLPVNSGQAQRVLCPSNSSQRVPLQAQKLVSSHKPV
          D.S.ENCISGPV.A..P.GGPK.VLVTQQFPCQNPLP.NSGQAQ.VLCPSNSSQRVPLQAQKLVSSHKPV
Retrocopy DQSEENCISGPVEAKTPAGGPKHVLVTQQFPCQNPLPANSGQAQWVLCPSNSSQRVPLQAQKLVSSHKPV

Parental  QNQKQKQLQATSVPHPVSRPLNNTQKSKQPLPSAPENNPEEELASKQKNEESKKRQWALEDFEIGRPLGK
          QNQKQKQLQATSVPHP.SRPLNNTQKSKQ...SAPENNPEEELASKQKNEESKKRQWALED.EIGRPLGK
Retrocopy QNQKQKQLQATSVPHPASRPLNNTQKSKQSPLSAPENNPEEELASKQKNEESKKRQWALEDLEIGRPLGK

Parental  GKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILE
          .KFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHL.HPNI.RLYGYFHDATRVYLILE
Retrocopy *KFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLQHPNIIRLYGYFHDATRVYLILE

Parental  YAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHA
          Y.PL.TV..ELQKLSKFDEQRTATYITELA.ALSYCHSK.VIHRDIKPENLLLGSAGEL.IA.FGWS.HA
Retrocopy YTPLETVNTELQKLSKFDEQRTATYITELASALSYCHSKPVIHRDIKPENLLLGSAGELEIANFGWSEHA

Parental  PSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVE
          PSSRRTTLCGTLDYLPPEMIEG..HDEKVDLWSLGVLC.EFLV.KPPFEANTYQETYKRISRVE
Retrocopy PSSRRTTLCGTLDYLPPEMIEGQIHDEKVDLWSLGVLCCEFLVRKPPFEANTYQETYKRISRVE

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	0.18 RPM	0.88 RPM
SRP007412_cerebellum	0.14 RPM	2.22 RPM
SRP007412_heart	0.55 RPM	1.46 RPM
SRP007412_kidney	0.37 RPM	1.60 RPM
SRP007412_liver	0.23 RPM	2.39 RPM
SRP007412_testis	0.32 RPM	83.36 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_381 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_381 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_381 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_510
Gorilla gorilla	retro_ggor_470
Pongo abelii	retro_pabe_231
Macaca mulatta	retro_mmul_431

---

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,