Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttttcaacaattaatctagacatatcacaagagctaaagattatatccaagcctattaacctgttttatccctcttttgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT

Basic information

species Oryza sativa
transcript LOC_Os05g36110.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G048150_T04 (Zea mays), 3'ss of exon 2
gtatgttttttcaacaattaatctagacatatcacaagagctaaagattatatccaagcctattaacctgttttatc--cctcttttgatt-tgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT
||||| ||   |||  |  |||  ||| |  |  ||    ||| |   |||||| | || || || ||||||||  |  |||  ||||  | ||||| ||||||||||||||  ||||||| ||||||||| |||| ||||||||| || | ||||||||||| |||||||| ||||| |||||||| || || |||
gtatgcttca-caaggaccaattcagatactttgcagtgactacaa--tatatctatgc-taatatcctgttttggctgcctactttgtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 2
-------gtatgttttttcaacaattaatctagacatatcacaagagctaaag--attatat-ccaagcctattaacctgttttatccctct---tttgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT
         |    ||  |||  | ||||  |||||  |  |||  |||| |   |  ||||    |  ||| || | | |||| || | ||   |||  ||||||| ||||||||||| ||  ||||||| |||||||||||||| ||||||||| |  | ||||||||||| |||||||| ||||| |||||||| || || |||
gtatgcttcacaagttcacaatgactaattcagacactttgcaatggctacaactacaatatattgatgctaatatcttcttttgtctccctactttttctttgcagTGTAGTTCTTTTGCCAATTGCTGTCACATTCTTCATCACTTGGTGGTTTATCCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 2
gtatgttttttcaacaattaatctagacatatcacaagagctaaagattatatccaagcctattaacctgttttatccctcttttgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT
          | |  ||  || |||  | |||    |    ||||  ||||   ||    |  |   ||  || ||     |||  || ||||||||||||||||| || ||||||||||| |||||||| || ||||||||| || ||||||||||||| || || |||||| | ||  | | ||| ||  | 
---------gtaatgaacaaaacta--cttattgagatgattaaattttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGGATA

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
gtatgttttttcaacaattaatctagacatatcacaaga-gctaaagattatatccaagcctattaacctgttttatccctcttttgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT
               |||  |   |   |  |    ||| | | ||  ||||   ||    |  |   ||  || ||     |||  || ||||||||||||||||| || ||||||||||| |||||||| || ||||||||| || ||||||||||||| || || |||||| | ||  | | ||| ||  | 
-------------gtaatggacaaaactacttattgagatgattaattttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtttttt-caacaattaatctagacatat-cacaagagctaaagattatatccaagcctattaacctgttttatccctcttttgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT
|||  |   |   | ||     | ||     || | || ||  | ||   | |         ||| |    | | ||      | |||  | | || || || || || ||||| |||||||||||| ||||||| ||||||||| |  |||| |||||||| || ||||||||  | || |  || |||||  ||
gtaaataactcgtagcaccctttttattttcatactcatgatttgaaatctttg--------tatcattggggtctaattgggtgttgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTT

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|29657648|gb|CB653923.1|CB653923
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|13896941|gb|AU183277.1|AU183277
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|33795379|gb|CF323560.1|CF323560
EST:     GTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: GTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|88740560|gb|CI764068.1|CI764068
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGT
EST: gi|1631723|gb|C19452.1|C19452
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|88732124|gb|CI757301.1|CI757301
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTT
EST: gi|88739463|gb|CI762971.1|CI762971
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCAT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCAT
EST: gi|29621889|gb|CB626900.1|CB626900
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|88759825|gb|CI769381.1|CI769381
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCAC
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCAC
EST: gi|88739598|gb|CI763106.1|CI763106
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTT
EST: gi|58695852|gb|CK084539.1|CK084539
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|88357088|gb|CI615975.1|CI615975
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|88343606|gb|CI622981.1|CI622981
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTG
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTG
EST: gi|29621929|gb|CB626940.1|CB626940
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|88745549|gb|CI768909.1|CI768909
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|88762333|gb|CI771889.1|CI771889
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCCTTCATCACCTGGTGGTTTG
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTC-TTCATCACCTGGTGGTTTG
EST: gi|87012610|gb|CI307358.1|CI307358
EST:     TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|88413003|gb|CI578854.1|CI578854
EST:     GTTTTGCTGTTCTTCAAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTAATCACCTGGTGGTTTGT
genomic: GTTTTGCTGTTCTTCAAA-GCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
EST: gi|88732046|gb|CI757223.1|CI757223
EST:     TGTNTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG                         CGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT
genomic: TGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATGgtatgttttt ... tgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaaagattatatccaagcctattaacctgttttatccctcttttgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT
                           cctgttttatccctct  CT-rich tract
     agattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttttttcaacaattaatctagacatatcacaagagctaaagattatatccaagcctattaacctgttttatccctcttttgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG