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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatcagtcgtatccaatttgtgtgacatgttttgtatcacactgaagaaagtttaaatattgctatcttgaatgtgctaagtataagatttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAGGAGACTGAAGAGGAGAAGAAAGCAGCAGAAGAACGGGCCGCAGCTGTCA

Basic information

species Oryza sativa
transcript LOC_Os03g29260.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g29260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 4
atatcagtcgtat-ccaatttgtgtgacatgttttgt-atcacactgaagaaagtttaaatattgct-atcttgaatgtgctaagtataagatttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAGGAGACTGAAGAGGAGAAGAAAGCAGCAGAAGAACGGGCCGCAGCTGTCA
         |||| |    | || |   ||||||| | || |   |   | ||  ||    ||||   |  ||  || ||  | || |  | |||      |||   | || |||||||||||||||||||| |||||||| || || || |||||||| |||||||| |||||||| || |||||  | || ||  ||||||
---------gtatgcttgatcgtctc-tatgttttctcataatgtttttgtaaagttgtgcattggggagatttcatatga-atgtgtgtgttttg----tagGATGCTGCGGCTGATGAAGAAGATGATGATGATGTTGACCTTTTCGGAGAGGAGACCGAAGAGGAAAAGAAAGCTGCTGAAGAGAGAGCAGCTTCTGTCA
















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|88402149|gb|CI614992.1|CI614992
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGGG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|58682390|gb|CK071077.1|CK071077
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|3768112|gb|AU032139.1|AU032139
EST:     GAAGGTTGAGTCAACTGCTTGTTCTGTGTCTNCA-CNTGCTGACCAAAAG                         GCANCAGCAAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGA
genomic: GAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAAC-TGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCA-GCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGA
EST: gi|88402165|gb|CI615008.1|CI615008
EST:     TGAAGGTTGAGTCACCTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGC-AGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGA
EST: gi|88339571|gb|CI641280.1|CI641280
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGG
EST: gi|88353429|gb|CI631614.1|CI631614
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCACCAGC
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGC
EST: gi|58606912|gb|CK034945.1|CK034945
EST:     AGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: AGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|88363300|gb|CI643158.1|CI643158
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|25799116|gb|CA755077.1|CA755077
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCNACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|88573347|gb|CI664918.1|CI664918
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTG
EST: gi|427633|gb|D23766.1|D23766
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|5851078|gb|AU078250.1|AU078250
EST:     TNAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|88395078|gb|CI609394.1|CI609394
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATTTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|87032231|gb|CI262013.1|CI262013
EST:     TGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|33805318|gb|CF328537.1|CF328537
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|88325561|gb|CI675368.1|CI675368
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|88354486|gb|CI628857.1|CI628857
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGA
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGA
EST: gi|88358923|gb|CI619427.1|CI619427
EST:     TGAAGGTTGAGTCAATTGGTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|218480642|gb|FG944950.1|FG944950
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|89167249|gb|CI252780.1|CI252780
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|55432415|gb|CV729228.1|CV729228
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|33813046|gb|CF332413.1|CF332413
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAG
EST: gi|88587802|gb|CI705577.1|CI705577
EST:     TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAG                         GCACCAGCAGCTGATGAAGAA
genomic: TGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAA

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: 72 (upstream exon), 75 (downstream exon)
Score: 72

TGGAGTTACCGCAGAGGGTGAAGGTGTGAAGGTTGAGTCAACTGCTTGTTCTGTGTCTCCAACTGCTGACCAAAAGgttaaaaatc ... ttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAGGAGACTGAAGAGGAGAAGAAAGCAGCAGAAGAACGGGCCGCAGCTGTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaagtttaaatattgctatcttgaatgtgctaagtataagatttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAGGAGACTGAAGAGGAGAAGAAAGCAGCAGAAGAACGGGCCGCAGCTGTCA
                                           atttaat  putative branch site (score: 72)
                                 taagtataagatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatcagtcgtatccaatttgtgtgacatgttttgtatcacactgaagaaagtttaaatattgctatcttgaatgtgctaagtataagatttaataccagGCACCAGCAGCTGATGAAGAAGATGATGACGATGTTGATCTGTTTGGTGAGGAGACTGAAGAGGAGAAGAAAGCAGCAGAAGAACGGGCCGCAGCTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - -acatgtt
- - - - - - - - - - - - - - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgtgc