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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCTCGACGGCGGCGGCAACAAGGGCTGGGGGATGAAGATATCCGTGAAGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctggtctccgcgctctcgatctgtcggtcgcgagcgccgatttcgtttctttctttttctttttcttttgtggggggcgatctaggaggtggt...

Basic information

species Oryza sativa
transcript LOC_Os09g24200.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24200.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G105772_T01 (Zea mays), 5'ss of exon 1
AGAGCTCGACGGCGGCGGCAACAAGGGCTGG--GGGATGAAGATATCCGTGAAGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctggtctccgcgctctcgatctgtcggtcgcgagcgccgatttcgtt-tctttctttttctttttcttttgtggggggcgatctaggaggtggt---
  || ||||||  |||||| ||   |||  |  | ||||||| | ||||||||||| ||||||||||| | |||||||||||| |||||  || |  | ||||||  |   |||    |||||| ||||||||||     |      | |   | | | ||       ||  |||  | |    ||  | | |    | | ||   
--AGTTCGACGCAGGCGGCGACGGCGGCGCGCCGAGATGAAGGTCTCCGTGAAGACGCTCAAGGGATCTAGCTTCCAGATCGAAGTGGAGCCCACCGACAAGgtactcatcggt---tgcgctcccgatctgtcg-ctatgtttctagttgctgatgtattggcggggctgcttcgctagatttggctgctttttaggtttgtttg

upper sequence: LOC_Os09g24200.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G061620_T05 (Zea mays), 5'ss of exon 1
AGAGCTCGACGGCGGCGGCAACAAGGGCTGGGGGATGAAGATATCCGTGAAGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctggtctccgcgctctcgatctgtcg-----gtcgcgagcgccgatttcgtttctttctttttctttttcttttgtggggggcgatctaggaggtggt--
|   |||     || ||    |   ||| | |  |||||| | ||||||||||| ||||||||||||| |||||| ||||| |||||  |  |  | |||||| ||    | |   |||||| ||||||||||     ||       || |  |   ||       |  |  ||   ||   | ||||    |||||||  |||   
AACCCTCCGGTTCGACGTAGGCGCCGGCGGCGAAATGAAGGTCTCCGTGAAGACGCTCAAGGGATCCAGCTTCCATATCGAAGTGGATCCTACCGACAAGgtaggc---agcccttgcgctcccgatctgtcgctatggttctagttgctggatgtattggcgggctgcttgttaggttcgtttgggg----tctaggatttggctg
















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|88410051|gb|CI573290.1|CI573290
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|58672603|gb|CK061289.1|CK061289
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88400724|gb|CI596145.1|CI596145
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|33691318|gb|CF319557.1|CF319557
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAG                         CAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|56157493|gb|D24336.3|D24336
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88317010|gb|CI625647.1|CI625647
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88316529|gb|CI622775.1|CI622775
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88377574|gb|CI605409.1|CI605409
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88717896|gb|CI739408.1|CI739408
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|58602384|gb|CK012912.1|CK012912
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|86884299|gb|CI311704.1|CI311704
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88693324|gb|CI736899.1|CI736899
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|29678389|gb|CB674664.1|CB674664
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88399554|gb|CI583288.1|CI583288
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88346546|gb|CI623003.1|CI623003
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88405923|gb|CI591318.1|CI591318
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|58609238|gb|CK037271.1|CK037271
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
EST: gi|88571905|gb|CI663278.1|CI663278
EST:     AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAG-A-                         -AGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT
genomic: AGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATT

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: 56 (upstream exon), 20 (downstream exon)
Score: 1

AGAGCTCGACGGCGGCGGCAACAAGGGCTGGGGGATGAAGATATCCGTGAAGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctg ... tttcttaaagCAGGTTGCTGATGTGAAAAGGATAATCGAGACTACTCAAGGACAGCACATTTACCCAGCTGAGCAACAGATGCTCATTCATCAGGGGAAGGTGCTCAAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCTCGACGGCGGCGGCAACAAGGGCTGGGGGATGAAGATATCCGTGAAGACACTCAAGGGATCCACCTTCCAGATCGAGGTGGACTCCGCGCAGAAGgtatgctctggtctccgcgctctcgatctgtcggtcgcgagcgccgatttcgtttctttctttttctttttcttttgtggggggcgatctaggaggtggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA