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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGCCTATGATGTGAGCATTAATGATGATACTTGGCCAAAGGAGGCATTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcatttcatgcagcatctctctgctatgtgattcattataaggtgttacaggaaatgactttatctttgttgcttctag

Basic information

species Oryza sativa
transcript LOC_Os01g01307.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01307.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G067476_T03 (Zea mays), 5'ss of exon 2
AACTGCCTATGATGTGAGCATTAATGATGATACTTGGCCAAAGGAGGCATTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcatttcatgcagcatctctctgctatgtgattcattataaggtgttacaggaaatgactttatctttgttgcttctag
 |||||||||||||||  ||||||||| ||  |||||||||  || |  |||||||||||| |||||||||  || ||||||||||||||||||||||||||||| |||||  |   |||| || ||||| |     |   | ||  ||   | ||  |||||  ||| |||   | |||  ||
GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacattttgtaatgcatatcactgctttacatgttcatgtacagt---aaagttaatga--ttaccttgact-ctttcag

upper sequence: LOC_Os01g01307.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G376727_T05 (Zea mays), 5'ss of exon 2
AACTGCCTATGATGTGAGCATTAATGATGATACTTGGCCAAAGGAGGCATTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcatttcatgcagcatctctctgctatgtgattcattataaggtgttacaggaaatgactttatctttgttgcttctag--
 |||||||||||||||    ||||||| ||  |||||||||   | ||||||||||||||| |||||||||  || ||||||||||||||||||||||||||||| |||||  |   ||||||||||||| | ||  |   | ||      ||||| |||||| || ||  || |  || ||    
GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacattttgtaatgcatctctctgctttatgtgttcatgtagatcagtacagaaaatgatttcattattttgactccttcag
















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|5002911|gb|AU068020.1|AU068020
EST:     TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCCACTG-TTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCA
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGT-CACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCA
EST: gi|87032410|gb|CI264191.1|CI264191
EST:     TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|25807463|gb|CA763424.1|CA763424
EST:     TNTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|86416814|gb|CI030825.1|CI030825
EST:     GGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: GGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|88975507|gb|CI021589.1|CI021589
EST:     GCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: GCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|87027081|gb|CI261528.1|CI261528
EST:     AAAGGCTTGACNC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: AAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|2797245|gb|AA750539.1|AA750539
EST:     TTTAAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTATCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|33660042|gb|CF291009.1|CF291009
EST:     GATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: GATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|58594778|gb|CF993086.1|CF993086
EST:     TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGAGGC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|86415979|gb|CI029990.1|CI029990
EST:     GATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: GATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|427829|gb|D23969.1|D23969
EST:     TTGAGCTTGATCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTGAGCTTG-TCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
EST: gi|5004937|gb|AU070175.1|AU070175
EST:     TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC                         TGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG
genomic: TTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAG

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), 75 (downstream exon)
Score: 121

AACTGCCTATGATGTGAGCATTAATGATGATACTTGGCCAAAGGAGGCATTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcat ... ttgcttctagTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGCCTATGATGTGAGCATTAATGATGATACTTGGCCAAAGGAGGCATTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCCgtgagtgcatttcatgcagcatctctctgctatgtgattcattataaggtgttacaggaaatgactttatctttgttgcttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG