RetrogeneDB ID: retro_olat_13

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 24:6096494..6097088(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000012619
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHOA
• Ensembl ID: ENSORLG00000018734
• Aliases: None
• Description: None

Sequence

>retro_olat_13
ATGGCAGACATACGGAAGAAGCTGGTGGTGGTCGGGGATGGCGCATGCGGGAAAACGTGTCTGCTCATTGTGTTTAGCAG
GGACGAGTTCCCCGAAGTGTACGTTCCGACTGTGTTTGAGACGTATGTGGCGGACATTGAGGTGGACAACAACAAGCAGG
TCCAGCTTGCTTTGTGGGACACGGCCGGACAGGAAGACTACGACCGCCTGCGCCCGCTCTCCTACCCGGACACTGATGTC
ATCCTCATGTGTTTCTCCGTGGACAGCCCCGACTCGCTGCAAAACATCCCGGAAAAGTGGGTCCCCGAGGTGAAACACTT
TTGCCCGAACGTGCCGATTATTCTGGTGGGCAACAAGAAGGACCTGCGCAACGACGAAAACACCAAGAACGAGCTGTCTC
GCTTGAAGCTGGAGCCCGTGAAGGCGGAGGACGGACGCGCCATGGCGGCGCGTATCGGCGCCTATGACTATTTGGAGTGC
TCTGCCAAAACCAAAGAGGGGATCTGGGAGGTTTTTGAAACGGCAACGCGAGCGGCCTTGCAAAAGCGGAGAACACCCGG
AGATGGTTGTTTTAAATGCTGCGTTTTAATGTGA

Alignment

ORF - retro_olat_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.24 %
• Parental protein coverage: 94.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDG-KQVELALWDTAGQEDYDRL
          MA.IRKKLV.VGDGACGKTCLLIVFS.D.FPEVYVPTVFE.YVADIEVD..KQV.LALWDTAGQEDYDRL
Retrocopy MADIRKKLVVVGDGACGKTCLLIVFSRDEFPEVYVPTVFETYVADIEVDNNKQVQLALWDTAGQEDYDRL

Parental  RPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPV
          RPLSYPDTDVILMCFS.DSPDSL.NIPEKW.PEVKHFCPNVPIILVGNKKDLRNDE.T..EL...K.EPV
Retrocopy RPLSYPDTDVILMCFSVDSPDSLQNIPEKWVPEVKHFCPNVPIILVGNKKDLRNDENTKNELSRLKLEPV

Parental  KPEDGRDMANRIGASGYMECSAKTKDGVREVFEMATRAALQARR
          K.EDGR.MA.RIGA..Y.ECSAKTK.G..EVFE.ATRAALQ.RR
Retrocopy KAEDGRAMAARIGAYDYLECSAKTKEGIWEVFETATRAALQKRR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryzias latipes was not studied using RNA-Seq expression data.

ChIP-Seq

Oryzias latipes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_olat_13 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_13 has 3 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_9
Takifugu rubripes	retro_trub_19
Tetraodon nigroviridis	retro_tnig_2

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023066	2 retrocopies	retro_cfam_1652, retro_cfam_186,
Callithrix jacchus	ENSCJAG00000003904	3 retrocopies	retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Dipodomys ordii	ENSDORG00000003382	3 retrocopies	retro_dord_1, retro_dord_18, retro_dord_538,
Gadus morhua	ENSGMOG00000008188	1 retrocopy	retro_gmor_18,
Myotis lucifugus	ENSMLUG00000013911	6 retrocopies	retro_mluc_108, retro_mluc_193, retro_mluc_1976, retro_mluc_2553, retro_mluc_2554, retro_mluc_2555,
Macaca mulatta	ENSMMUG00000012962	1 retrocopy	retro_mmul_977,
Monodelphis domestica	ENSMODG00000012981	2 retrocopies	retro_mdom_19, retro_mdom_294,
Oreochromis niloticus	ENSONIG00000018884	1 retrocopy	retro_onil_32,
Oryzias latipes	ENSORLG00000018734	1 retrocopy	retro_olat_13 ,
Sarcophilus harrisii	ENSSHAG00000016308	2 retrocopies	retro_shar_60, retro_shar_96,
Ictidomys tridecemlineatus	ENSSTOG00000004561	2 retrocopies	retro_itri_39, retro_itri_96,
Takifugu rubripes	ENSTRUG00000011944	1 retrocopy	retro_trub_19,
Tarsius syrichta	ENSTSYG00000008220	3 retrocopies	retro_tsyr_1604, retro_tsyr_413, retro_tsyr_593,