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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACACAGGTTCTTGCTCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatgctttaacctacatgtacattcattcatttatttgactgcagatctcactattttttttattgacaatctgcag

Basic information

species Oryza sativa
transcript LOC_Os02g58340.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G133919_T01 (Zea mays), 5'ss of exon 13
TCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACACAGGTTCTTGCTCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatgctttaacctacatgtacattcattcatttatttgactgcagatctcactattttttttattgacaatctgcag
|||||||||||||| |||| ||||||||| || || ||||| |||||||||||||| |||||||| | |||||||||||||||||||||||| |||||||||||||    || |   ||   | |    ||  |||  |   |||| | |   |     ||||  || || | |||| |||||
TCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACACAAGTTCTTGCTCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgccactcttttctctctct---ctctctcaagttggtgacaggatgacctctcatttcatt-atgggcaat-tgcag

upper sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA09G33490.1 (Glycine max), 5'ss of exon 13
TCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACACAGGTTCTTGCTCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatgctt-taacctacatgtacattcattcatttatttgactgcagatctcactatttttttta---ttgacaatctgcag
|| || |||||||| ||||| |||||| |||||  ||| || ||  || ||||  | || |||||||  ||||| ||||||||||||||||||||||||||||||   ||| | |    |   | |  | | || |   | | | |    |  |     ||||| || |    ||  |  |    ||
TCAATCTATGATGTTGACCGCAGAGTTTCTGAGAAAACCCAAGTGATTCCTCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgatgtgcctcttgtttctctttgtaattatgctagtgtctcaacaaaactaaatttatttattctgggttttgcttttgttag

upper sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA01G02480.1 (Glycine max), 5'ss of exon 13
TCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACACAGGTTCTTGCTCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatgctt-taacctacatgtacattcattcatttatttgactgcagatctcactatttttttta---ttgacaatctgcag
|| || |||||||| ||||  |||||| |||||  ||| || ||  || ||||  | || |||||||  ||||| |||||||||||||||||||||||||||||||  ||| | |    |   | |  | | || |   | | | |    |  |     ||||| || |    ||  || |    ||
TCGATCTATGATGTTGACCACAGAGTTTCTGAGAAAACCCAAGTGATTCCTCCATTACCAGAGGATAGGTTCCTTTGCAGCTTTAGCCATATATTTGCAGgtttgctgtgcctcttgtttctctttgtaattatgctagtgtctcaacaaaactaaatttatttattctgggttttgcatttgttag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|87010666|gb|CI312358.1|CI312358
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|86489837|gb|CI132470.1|CI132470
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|29685086|gb|CB681361.1|CB681361
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|27577469|gb|CB000164.1|CB000164
EST:     TCCCCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|86525997|gb|CI166203.1|CI166203
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|86437668|gb|CI119588.1|CI119588
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|88415868|gb|CI536022.1|CI536022
EST:     GCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: GCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|29628315|gb|CB633326.1|CB633326
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|86596740|gb|CI286653.1|CI286653
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|89183340|gb|CI045905.1|CI045905
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|29629259|gb|CB634270.1|CB634270
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|86497160|gb|CI139793.1|CI139793
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|88223547|gb|CI223396.1|CI223396
EST:     TAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|87005786|gb|CI316205.1|CI316205
EST:     CCTGTGCAGCTTTAGCCATATATTTCCAG                         GAGGCTAGGCAGCTGGATACTACAGTTACAAG
genomic: CCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|86906176|gb|CI320107.1|CI320107
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|86889992|gb|CI319981.1|CI319981
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTGGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|88907988|gb|CI090584.1|CI090584
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|88220405|gb|CI219965.1|CI219965
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|163920194|gb|EG714428.1|EG714428
EST:     CATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: CATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|87040458|gb|CI195080.1|CI195080
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|87036488|gb|CI191110.1|CI191110
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|88996615|gb|CI389281.1|CI389281
EST:     TATATTTGCAG                         GAGGCTATGCAGCT-GATACTACAGTTACAAG
genomic: TATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|58613168|gb|CK040880.1|CK040880
EST:     TTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|87021331|gb|CI295390.1|CI295390
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|88254054|gb|CI352680.1|CI352680
EST:     TAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|87041614|gb|CI196236.1|CI196236
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|86862960|gb|CI331761.1|CI331761
EST:     GCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: GCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|22306852|gb|BQ908074.1|BQ908074
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|22305323|gb|BQ906545.1|BQ906545
EST:     CCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: CCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTG-CAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|66912656|gb|CX099504.1|CX099504
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|38471500|gb|CF955631.1|CF955631
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|88271562|gb|CI387615.1|CI387615
EST:     TAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|88220356|gb|CI219916.1|CI219916
EST:     CCTCTTCCGGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: CCTCTTCC-GGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|18387237|gb|BM420435.1|BM420435
EST:     CTCTTCCGGAGGATAAATTCCTGTNGCAGCTTTAGCCATGATATTTGCAG                         GAGGCTATGCAGCTGGATACTGACAGTTGACAAG
genomic: CTCTTCCGGAGGATAAATTCCTGT-GCAGCTTTAGCCAT-ATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACT-ACAGTT-ACAAG
EST: gi|89174907|gb|CI111105.1|CI111105
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|88843719|gb|CI010977.1|CI010977
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|58610594|gb|CK038306.1|CK038306
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|313084093|gb|HO213876.1|HO213876
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG
EST: gi|9864982|gb|AU100732.1|AU100732
EST:     TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAG                         GAGGCTATGCAGCTGGATACTACAGTTACAAG
genomic: TCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 64 (upstream exon), 69 (downstream exon)
Score: 65

TCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACACAGGTTCTTGCTCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatg ... caatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACACAGGTTCTTGCTCCTCTTCCGGAGGATAAATTCCTGTGCAGCTTTAGCCATATATTTGCAGgtttgcaatgctttaacctacatgtacattcattcatttatttgactgcagatctcactattttttttattgacaatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT