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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacatttgaagtagtttgtaaaaattctctctctgacccaataatgcttgtttggttaatgtacatgtctacatgagtgatatgggttgatgaaatcgtacgttttcttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAGAAGTTCCTGGAGAAGAACGATGTGTGCGCAATGATCCAAGCCTGTGATG

Basic information

species Oryza sativa
transcript LOC_Os12g02094.1
intron # 5
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|112786000|gb|EE591849.1|EE591849
EST:     TTCAATTACTACTCAAGGAATGCACCAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTATGCAGTACGTCCCTCTGGTTTTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88420045|gb|CI513802.1|CI513802
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGTTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGCG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88286128|gb|CI515252.1|CI515252
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGCG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88480954|gb|CI418225.1|CI418225
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|33674097|gb|CF302336.1|CF302336
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|86875076|gb|CI322291.1|CI322291
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88288269|gb|CI515413.1|CI515413
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGCG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88374299|gb|CI513386.1|CI513386
EST:     AAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTTTAGTGAACGGTGAG
genomic: AAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|33685698|gb|CF313937.1|CF313937
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88319373|gb|CI515834.1|CI515834
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGCG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88288199|gb|CI515343.1|CI515343
EST:     TGCAACAAGATTGAAGGTCATCACCACCAG                         TGCAAGAGGATGGTTCTCCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88843358|gb|CI372258.1|CI372258
EST:     CAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: CAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|163920568|gb|EG714508.1|EG714508
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCATCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCT
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCT
EST: gi|88965963|gb|CI006739.1|CI006739
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|5803366|gb|AI978314.1|AI978314
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|86871914|gb|CI332086.1|CI332086
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|86871216|gb|CI328418.1|CI328418
EST:     TCAATTACTACTGCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TCAATTACTACT-CAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88902054|gb|CI374662.1|CI374662
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTCCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|3759064|gb|C96763.1|C96763
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|86903545|gb|CI323028.1|CI323028
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|86873796|gb|CI341229.1|CI341229
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88319196|gb|CI513260.1|CI513260
EST:     TCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGCG
genomic: TCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88222925|gb|CI220671.1|CI220671
EST:     TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
genomic: TTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG
EST: gi|88462634|gb|CI517163.1|CI517163
EST:     TTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAG                         TGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGCG
genomic: TTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAG

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: 63 (upstream exon), 72 (downstream exon)
Score: 69

TTTGAGATCATTCAATTACTACTCAAGGAATGCAACAAGATTGAAGGTCATCAGCAGCAGgtaaaacatt ... ttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAGAAGTTCCTGGAGAAGAACGATGTGTGCGCAATGATCCAAGCCTGTGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtctacatgagtgatatgggttgatgaaatcgtacgttttcttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAGAAGTTCCTGGAGAAGAACGATGTGTGCGCAATGATCCAAGCCTGTGATG
                      ggttgat  putative branch site (score: 69)
                                        ttttcttgtt  putative PPT
                           atgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacatttgaagtagtttgtaaaaattctctctctgacccaataatgcttgtttggttaatgtacatgtctacatgagtgatatgggttgatgaaatcgtacgttttcttgttgacagTGCAAGAGGATGGTTCTGCAGTACGTCCCTCTGGTTCTAGTGAACGGTGAGAAGTTCCTGGAGAAGAACGATGTGTGCGCAATGATCCAAGCCTGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC