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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGTCTGGCACCAAAGACAGCTGACAGACAGTCTTCCATAGAACAGATTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttatgactaatttggacatgttatgtgggtag

Basic information

species Oryza sativa
transcript LOC_Os02g40830.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G064695_T03 (Zea mays), 5'ss of exon 7
-----------------------------------------------------TGATGGTCTGGCACCAAAGACAGCTGACAGACAGTCTTCCATAGAACAGATTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttatgactaatttggacatgttatgtgggtag
                                                     ||||||||| || | |||| |||| || || |||||||| |||||||||||||||||||| |||||||| |||||||||| |||||||||| |||| ||||||                                                                                     
GTTCCTATTGATGTATTTAAAGGAATCACAGATGAGGATGCAGCTAAAGTTGTTGATGgtctagctctaaaggcagcggataggcagtcttctatagaacagattaagaagctgtatgaacttttctgcaagtgtgattgcacattgctggaggtatg-----------------------------------------------------------------------------------

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G064695_T01 (Zea mays), 5'ss of exon 7
TGATGGTCTGGCACCAAAGACAGCTGACAGACAGTCTTCCATAGAACAGATTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttat----gact---------aatttggacatgttatgtgggtag
||||||||| || | |||| |||| || || |||||||| |||||||||||||||||||| |||||||| |||||||||| |||||||||| |||| ||||||  || | | ||| |||      ||||            |||  | | |  |  ||||    || |         ||||||||    | ||||||||||
TGATGGTCTAGCTCTAAAGGCAGCGGATAGGCAGTCTTCTATAGAACAGATTAAGAAGCTGTATGAACTTTTCTGCAAGTGTGATTGCACATTGCTGGAGgtatgcagtgagaaaaggtcctcattttgatgctttttatcttattattacgttttttatctgtgaatttgtactgtaatttggatgcttaatgtgggtag
















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|66913068|gb|CX099916.1|CX099916
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
EST: gi|163921201|gb|EG714126.1|EG714126
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAATCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
EST: gi|163929534|gb|EG713477.1|EG713477
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAATCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
EST: gi|29662328|gb|CB658603.1|CB658603
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
EST: gi|29662110|gb|CB658385.1|CB658385
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAG
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAG
EST: gi|13420568|gb|AU174658.1|AU174658
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCA
EST: gi|33794775|gb|CF323267.1|CF323267
EST:     TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAAACA-GCTGGTCGCTGCTGATGC
genomic: TTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAA-CAAGCTGGTCGCTGCTGATGC
EST: gi|27577186|gb|CA999880.1|CA999880
EST:     TAAGAAGCTCTATGAACTGTTCTGNCAA-TCTGATTGCACACTGCTCGAG                         ATTAATCCTCTTGCTGAGACAGCTGACAAACA-GCTGGTCGCTGCTGATGC
genomic: TAAGAAGCTCTATGAACTGTTCTG-CAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAA-CAAGCTGGTCGCTGCTGATGC

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: 74 (upstream exon), 75 (downstream exon)
Score: 59

TGATGGTCTGGCACCAAAGACAGCTGACAGACAGTCTTCCATAGAACAGATTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaata ... atgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGGTCTGGCACCAAAGACAGCTGACAGACAGTCTTCCATAGAACAGATTAAGAAGCTCTATGAACTGTTCTGCAAGTCTGATTGCACACTGCTCGAGgtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttatgactaatttggacatgttatgtgggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC