Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACTTCCTCTCAGTGTTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatccttttttatatgggttcatggccaaagcatttcaatccatgttcaatagctactactactatattttcgatggtacacgctccatggttccttaactgctgtacag

Basic information

species Oryza sativa
transcript LOC_Os05g09550.3
intron # 5
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g09550.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G117388_T01 (Zea mays), 5'ss of exon 6
CTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACTTCCTCTCAGTGTTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatccttttttatatgggttcatggccaaagcattt-----caat---------------ccatgttcaatagctactactactatattttcgatggtacacgctccatggttccttaac-tgctgtacag--------
|||| |||||||| ||  | ||||||||    ||||||||| |  ||||||||||||| || |||||||| |||| |||||| ||||| || |  ||||||||||||||  || ||||  |||||| |||| ||||      || |               | | | |||||  || | | || | || ||| ||   |    || || ||  |||||||| ||||| ||          
CTGGACTTCTGGGTATCATGGTTGGACATCTCTACTACTTCTTTGCAGTGTTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGGTgtatccttt--tacatgg--tcatggtcaaaacattctctcgcagttttcatatacaacgactaagatcaatttctgcaaatattttagttttgaatatctctgcaccttgtctccttaacctgctgcactcttgcacag

upper sequence: LOC_Os05g09550.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G143817_T01 (Zea mays), 5'ss of exon 6
CTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACTTCCTCTCAGTGTTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatccttttttatatgggttcatggccaaagcatt-----tcaatccatgt------------tcaata-----gctactactactatattttcgatggtacacgctccatggttccttaac-tgctgtacag------
| ||||||||||| ||  | ||||||||    ||||||| | |  ||||||||||||| || |||||||||||||||||||| ||||| || |  ||||||||||||||  || ||||  ||||||||||||||||     ||| |     |            |||||      ||||   ||||| ||||||  |   ||   ||||| ||  |||||||| ||||| ||        
CAGGCCTTCTGGGTATCATGGTTGGACATCTATACTACTACTTTGCAGTGTTGCACCCTCTCGCCACCGGAAAGAACTACCTCAAGACTCCGAAATGGGTgtatccttt--tacatgg--tcatggccaaagcattatctctcagtttgcatatacaactgagatcaatttctgcgctatggctactttattttttaatatatctgctccttgtctccttaacctgctgcacttgcacag

upper sequence: LOC_Os05g09550.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G117388_T02 (Zea mays), 5'ss of exon 6
--CTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACTTCCTCTCAGTGTTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatccttttttatatgggttcatggccaaagcattt-----caat---------------ccatgttcaatagctactactactatattttcgatggtacacgctccatggttccttaac-tgctgtacag--------
  |||| |||||||| ||  | ||||||||    ||||||||| |  ||||||||||||| || |||||||| |||| |||||| ||||| || |  ||||||||||||||  || ||||  |||||| |||| ||||      || |               | | | |||||  || | | || | || ||| ||   |    || || ||  |||||||| ||||| ||          
GCCTGGACTTCTGGGTATCATGGTTGGACATCTCTACTACTTCTTTGCAGTGTTGCACCCTCTTGCCACCGGGAAGAGCTACCTCAAGACTCCTAAATGGgtgtatccttt--tacatgg--tcatggtcaaaacattctctcgcagttttcatatacaacgactaagatcaatttctgcaaatattttagttttgaatatctctgcaccttgtctccttaacctgctgcactcttgcacag

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|29671730|gb|CB668005.1|CB668005
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|86544097|gb|CI184303.1|CI184303
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|27578253|gb|CB000948.1|CB000948
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|88240020|gb|CI239182.1|CI239182
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|86527518|gb|CI167724.1|CI167724
EST:     TTGCA-CCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|88440632|gb|CI552098.1|CI552098
EST:     TGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|88241377|gb|CI241226.1|CI241226
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACAAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|88851269|gb|CI404321.1|CI404321
EST:     TACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|86880056|gb|CI340053.1|CI340053
EST:     TAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|86503965|gb|CI146598.1|CI146598
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|44669030|gb|CR282464.1|CR282464
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|88208878|gb|CI206729.1|CI206729
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|86501898|gb|CI144531.1|CI144531
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|88225634|gb|CI225550.1|CI225550
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|86258911|gb|CI004455.1|CI004455
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|86526253|gb|CI166459.1|CI166459
EST:     TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
EST: gi|38476086|gb|CF960219.1|CF960219
EST:     TTGCACCCGCTAGCCACCGGAGGGAACTACCTGAAGACACCAATGTGGGT                         ACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT
genomic: TTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGT

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: 69 (upstream exon), 68 (downstream exon)
Score: 45

CTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACTTCCTCTCAGTGTTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatcctttt ... tgctgtacagACATAAGATTGTTGCTCGATTCAGAATAGGTGTGCAGGCGAACGCTCCGGTCCGACCCGCGGCCGCCAACACCGGATCAGGCGCCTTCAGAGGAAGGAGC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGCCTTCTGGGAATTCTCGTTGGACACACGTACTACTTCCTCTCAGTGTTGCACCCGCTAGCCACCGGAAAGAACTACCTGAAGACACCAATGTGGGTgtatccttttttatatgggttcatggccaaagcatttcaatccatgttcaatagctactactactatattttcgatggtacacgctccatggttccttaactgctgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA