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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatatcaagtttgcattttgcaatataggtgcatataacatatttacttgtcacagtctgtgcaaggagcacgtataatttttcttcatttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCGAGTCAAGAACTGGTTTACGTTTAATGAGCCAAGGATAGTAGCAGCACTT

Basic information

species Oryza sativa
transcript LOC_Os03g49610.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC217401.3_FGT002 (Zea mays), 3'ss of exon 5
aaatatcaagtttgcattttgcaatataggtg-catataacatatttacttgtcacagtctgtgcaaggagcacgtataatttttcttcatttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCGAGTCAAGAACTGGTTTACGTTTAATGAGCCAAGGATAGTAGCAGCACTT
|| | | |||| ||| | | | ||| | | || ||| | | ||| ||| | ||||| | | | | | | | | | || ||||| | ||||| | ||||||||||| |||||||||||||| | |||| ||||||||||||||||||| || || ||||||||||||||||||||| |||
aactgtgaagtg-atattgttctttttagataatacatttcatttgttcttatcataatctgtactgaggataggccttttctggatattatgttctgcagGGACATATTTGCTGACTATGCTGATTTTTGTTTCAAGACTTTTGGCAATCGAGTCAAGAACTGGTTCACATTAAATGAGCCAAGGATAGTAGCATTCCTT
















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|58658600|gb|CK047280.1|CK047280
EST:     TTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTGTGTTTCAAGACATATGGCGATCG
genomic: TTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58670861|gb|CK059547.1|CK059547
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         AGGTGTATTTTCGGACTATGCTGA
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGA
EST: gi|58673207|gb|CK061893.1|CK061893
EST:     TTGCCACCTTCCAGAAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: T-GC-AC-TTC-AGAAAAA-GTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58666291|gb|CK054977.1|CK054977
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58662636|gb|CK051322.1|CK051322
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         AGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58672509|gb|CK061195.1|CK061195
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58653737|gb|CK042417.1|CK042417
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|117229561|gb|CT859875.1|CT859875
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58671028|gb|CK059714.1|CK059714
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58663559|gb|CK052245.1|CK052245
EST:     CCACTTGCACTTCAGAAAAAGTATGCAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58664913|gb|CK053599.1|CK053599
EST:     CCACTTGCACTTCAGAAAACGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58678605|gb|CK067292.1|CK067292
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAGAAATTGT                         TGGTGTATTTGCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58654026|gb|CK042706.1|CK042706
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58678530|gb|CK067217.1|CK067217
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58670130|gb|CK058816.1|CK058816
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTGGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58612072|gb|CK039784.1|CK039784
EST:     CACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAGGTTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATC
genomic: CACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAA-ATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATC

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: 75 (upstream exon), 73 (downstream exon)
Score: 26

GGCTTATTCCTTACGTCAATCTGAACCACTACGATCTCCCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCGAGTCAAGAACTGGTTTACGTTTAATGAGCCAAGGATAGTAGCAGCACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttgtcacagtctgtgcaaggagcacgtataatttttcttcatttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCGAGTCAAGAACTGGTTTACGTTTAATGAGCCAAGGATAGTAGCAGCACTT
                                  tttttcttcatttttt  CT-rich tract
 tataatttttcttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatatcaagtttgcattttgcaatataggtgcatataacatatttacttgtcacagtctgtgcaaggagcacgtataatttttcttcatttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCGAGTCAAGAACTGGTTTACGTTTAATGAGCCAAGGATAGTAGCAGCACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - -gtttgca
- - - - - - - - ttttgca
- - - - - - - - - - - - - - -gtgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcaag