RetrogeneDB ID: retro_olat_10

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: scaffold1046:23312..24452(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000020561
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SPAST
• Ensembl ID: ENSORLG00000012235
• Aliases: None
• Description: None

Sequence

>retro_olat_10
CTAGGAAGCAACTTCAAAACGGCGCGTGAGCAATTTATTGTTGATCAACAGAAAAAATGTTCTCAGCAGTCGCGGGGAGC
CCAGGCCTTTGGGATGACTGCAACTGTGAAGAAATCTCTGGGCGCCAACAGGCCTCGGGGCACATTCTCAAAATTTGTGT
CACCCATCCCACGACAGGAGGATGAAGACAATGCGGCAAGTCAAAGTTCCACACAGGAACCTCCAATCCTGGACGAGCGT
CTGAAAAACTTTGAGCCAAAGATAATTGAGCTGATCATGAGTGAGATCATGGACCACGGGCCTCCCATTGGCTGGGATGA
CATCGCGGGGCTGGAGTTTGCCAAGAACACCATCAAGGAGATAGTGGTCTGGCCAATGCTCCGACCTGATATCTTTACTG
GTCTCAGAGGGCCCCCCAAAGGTATCCTGTTGTTCGGGCCCCCAGGAACTGGAAAAACTCTTATTGGAAAATGCATTGCT
TGTCAGTCAGGCGCCACTTTCTTTAGCATCAGCGCTTCGTCCCTTACATCCAAGTGGGTGGGTGAAGGAGAAAAAATGGT
GCGAGCCCTATTTGCCATTGCTGGCTGTCACCAACCTGCCGTCATCTTCATCGATGAAATCGACTCCCTGTTGTCCCAGC
GTACAGACGGGGAGCACGACTCTTCGCGCAGGATCAAGACAGAGTTCTTGGTTCAACTGGACGGTGCAGCCACTGCATCA
GAGGACCGCATCCTGGTGGTGGGGGCCACTAACCGGCCCCAGGAGATTGATGAGGCCGCTCGCAGACGTTTGGCCAAGCG
GCTCTATATCCCCCTTCCTGAAGCAGCAGCCCGACGGCAGATAGTGTTCAACCTCATGGCCCAAGAGAAAAGCCAGTTGA
GAGAGCCGGAGCTGGAAAGCGTGGTGAGGGCCACAGAGGGCTTCTCCGGCGCTGACATGACGCAGCTCTGCAGGGAGGCA
GCTTTGGGACCAATTCGCAGCATCCAGCTTAGTGACATCGCCACCATCACTGCAGATCAGGTGCGGCCGATTCTATTCAG
TGACTTCCAGGAGGCTCTGAAGACTGTTCGACCCAGTGTCTCTGCCAAAGACCTGGAGCTCTATGAGGAGTGGAATCAGA
CTTTTGGATGTGGACGCTAA

Alignment

ORF - retro_olat_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.48 %
• Parental protein coverage: 61. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQPKRDMKNFKNVDSKLANLIMNEIVDRGSSVCFDDIAGQARAKQALQEIVILPALRPELFTGLRAPARG
          Q.P.......KN...K...LIM.EI.D.G.....DDIAG...AK....EIV..P.LRP..FTGLR.P..G
Retrocopy QEPPILDERLKNFEPKIIELIMSEIMDHGPPIGWDDIAGLEFAKNTIKEIVVWPMLRPDIFTGLRGPPKG

Parental  LLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSVIFIDEVDSLL
          .LLFGPPG.GKT...K..A..S.ATFF.ISA.SLTSK.VGEGEK.VRALFA.A...QP.VIFIDE.DSLL
Retrocopy ILLFGPPGTGKTLIGKCIACQSGATFFSISASSLTSKWVGEGEKMVRALFAIAGCHQPAVIFIDEIDSLL

Parental  CERREGEHDASRRLKTEFLIEFDGVQSGGDDRVLVMGATNRPQELDEAILRRFAKRIYVSLPDEKTRFTL
          ..R..GEHD.SRR.KTEFL...DG......DR.LV.GATNRPQE.DEA..RR.AKR.Y..LP....R...
Retrocopy SQRTDGEHDSSRRIKTEFLVQLDGAATASEDRILVVGATNRPQEIDEAARRRLAKRLYIPLPEAAARRQI

Parental  LKNLLGKHGNPLGTNDITYLSKVTAGFSGSDLTSLAKDAALGPIRELGPDQVRNMSASEVRNIQKKDFED
          ..NL.......L...........T.GFSG.D.T.L...AALGPIR...........A..VR.I...DF..
Retrocopy VFNLMAQEKSQLREPELESVVRATEGFSGADMTQLCREAALGPIRSIQLSDIATITADQVRPILFSDFQE

Parental  SLKRIKPTVSPATLDMYAKWNKEFG
          .LK...P.VS...L..Y..WN..FG
Retrocopy ALKTVRPSVSAKDLELYEEWNQTFG

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

1 EST(s) were mapped to retro_olat_10 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DK198050	23800	24069	100	269	0	269

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_10 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_10 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000007400	1 retrocopy	retro_lafr_1056,
Myotis lucifugus	ENSMLUG00000015352	1 retrocopy	retro_mluc_1873,
Oryzias latipes	ENSORLG00000012235	1 retrocopy	retro_olat_10 ,
Takifugu rubripes	ENSTRUG00000000131	1 retrocopy	retro_trub_21,