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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttgatttcgatggaatcaaatgtctagtggcttgcttttttgttctaagatggccaatcatgactagtgttgctgatttgtgatgcttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGGGGAGGATATGGTGTTCTACTTCAAGGTGCGGCCCGAGGCCGGCGACTAC

Basic information

species Oryza sativa
transcript LOC_Os05g13440.1
intron # 1
splice site 3'
intron type U2

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|88321824|gb|CI672969.1|CI672969
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88727931|gb|CI749443.1|CI749443
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|218480637|gb|FG944945.1|FG944945
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCNGGGCGAGCGACTTGT
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGC-GGGCGAGCGACTTG-
EST: gi|88436600|gb|CI691330.1|CI691330
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88570263|gb|CI661438.1|CI661438
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|58663146|gb|CK051832.1|CK051832
EST:     TTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: TTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|33659404|gb|CF282017.1|CF282017
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|33808581|gb|CF330176.1|CF330176
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88349520|gb|CI653799.1|CI653799
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88342124|gb|CI636482.1|CI636482
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88458337|gb|CI695723.1|CI695723
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88583096|gb|CI700553.1|CI700553
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGAATTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88582454|gb|CI699868.1|CI699868
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88588559|gb|CI706384.1|CI706384
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88440830|gb|CI693400.1|CI693400
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTCCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88376943|gb|CI639268.1|CI639268
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88959372|gb|CI685853.1|CI685853
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88364521|gb|CI644599.1|CI644599
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|58683841|gb|CK072528.1|CK072528
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88448536|gb|CI693924.1|CI693924
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88344646|gb|CI637255.1|CI637255
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGANTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88723267|gb|CI746777.1|CI746777
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88336614|gb|CI656885.1|CI656885
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|163926796|gb|EG715084.1|EG715084
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCAATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|88585605|gb|CI703248.1|CI703248
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
EST: gi|396941371|gb|HO188580.1|HO188580
EST:     CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTG                         ATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG
genomic: CTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGG

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: 73 (upstream exon), 62 (downstream exon)
Score: 69

ATCCTCCCTCTCTTTCGCTCGTAGCCATCGCTCTCTTCCACTGGTTCGCTCTCTCCGTCAAACCGTTTGGTTTCGCCGCCTCTCTCCGTTGAGCTCTCTGgtaagggcta ... ttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGGGGAGGATATGGTGTTCTACTTCAAGGTGCGGCCCGAGGCCGGCGACTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctaagatggccaatcatgactagtgttgctgatttgtgatgcttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGGGGAGGATATGGTGTTCTACTTCAAGGTGCGGCCCGAGGCCGGCGACTAC
                             tgctgat  putative branch site (score: 69)
                                             ttatgaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttgatttcgatggaatcaaatgtctagtggcttgcttttttgttctaagatggccaatcatgactagtgttgctgatttgtgatgcttatgaacagATTTTTCCCCGTGCACTACTCGATCTGCTCCGGGCGGGCGAGCGACTTGGGGGAGGATATGGTGTTCTACTTCAAGGTGCGGCCCGAGGCCGGCGACTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
tttcttg
- - - - - - - - gaatcaa
- - - - - - - - - - - - - - - - ggcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgatgc