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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccatgttgtgatttcagaacaaatgccatctgactgtcgcgatctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcagacag

Basic information

species Oryza sativa
transcript LOC_Os01g14860.4
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 3
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccat---gttgtgatttcagaacaaatgc-catctgactgtcgcg-atctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcagacag
||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || |||||||||| | | | |   |||    |  ||||||   ||| | |   ||| |   |   ||   ||||||  |  | || ||   | |||  | | | |||  ||||                            
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctttactgcatttgatcatgatttatcaactattctacatgtttttagtgcatgtctgaatctaataattgagagtcaag--accataatt--taat----------------------------

upper sequence: LOC_Os01g14860.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 3
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccatgttgtgatttcagaacaaatgc-catctgactgtcgcgatctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcagacag
||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || ||||||| || | | | |   ||| |  | ||     ||||  ||  ||| |   |   ||| |||  |||     | |      ||||| |    |||   | | |||  | |                    
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctttactgcatttgattatc----aacagctgtgcatgtttttagtgcgttcttgaatcaaatagctg----aaagccaagaacataatttaatgagctac--------------------
















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|5003279|gb|AU068428.1|AU068428
EST:     CCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: CCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|58661642|gb|CK050322.1|CK050322
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58661642|gb|CK050322.1|CK050322
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58661642|gb|CK050322.1|CK050322
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58661642|gb|CK050322.1|CK050322
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58661642|gb|CK050322.1|CK050322
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|86596734|gb|CI286647.1|CI286647
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|58685932|gb|CK074619.1|CK074619
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58685932|gb|CK074619.1|CK074619
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58685932|gb|CK074619.1|CK074619
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58685932|gb|CK074619.1|CK074619
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58685932|gb|CK074619.1|CK074619
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58654229|gb|CK042909.1|CK042909
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCGGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|163921584|gb|EG712155.1|EG712155
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|163921584|gb|EG712155.1|EG712155
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|163921584|gb|EG712155.1|EG712155
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|163921584|gb|EG712155.1|EG712155
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|163921584|gb|EG712155.1|EG712155
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|29687086|gb|CB683361.1|CB683361
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|58665103|gb|CK053789.1|CK053789
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|58652484|gb|CK041164.1|CK041164
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         TTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacagTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCT
EST: gi|58665294|gb|CK053980.1|CK053980
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|29618976|gb|CB623988.1|CB623988
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|58590979|gb|CF989287.1|CF989287
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|58598975|gb|CK009503.1|CK009503
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58598975|gb|CK009503.1|CK009503
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58598975|gb|CK009503.1|CK009503
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58598975|gb|CK009503.1|CK009503
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58598975|gb|CK009503.1|CK009503
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58676495|gb|CK065182.1|CK065182
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|2317492|gb|C22546.1|C22546
EST:     GGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|33796677|gb|CF324206.1|CF324206
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|33796677|gb|CF324206.1|CF324206
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|33796677|gb|CF324206.1|CF324206
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|33796677|gb|CF324206.1|CF324206
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|33796677|gb|CF324206.1|CF324206
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58653056|gb|CK041736.1|CK041736
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|58671331|gb|CK060017.1|CK060017
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|58674441|gb|CK063127.1|CK063127
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58674441|gb|CK063127.1|CK063127
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58674441|gb|CK063127.1|CK063127
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58674441|gb|CK063127.1|CK063127
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58674441|gb|CK063127.1|CK063127
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         A
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacag-
EST: gi|58657986|gb|CK046666.1|CK046666
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga
EST: gi|58673516|gb|CK062202.1|CK062202
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGACAG                      
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-ACAGgtgatttcct ... ttgcaga

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: 73 (upstream exon), 48 (downstream exon)
Score: 3

GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... ttgcagacagTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccatgttgtgatttcagaacaaatgccatctgactgtcgcgatctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcagacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG