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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATGCTTCTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgcactactccttttcatgacctttactttgcatgcaactccatgaggttgcaaaatgcactggatggtactccttctgttttcatataattat...

Basic information

species Oryza sativa
transcript LOC_Os09g06970.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06970.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G123807_T02 (Zea mays), 5'ss of exon 3
AGCATGCTTCTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgcactactccttttcatgacctttactttgcatgcaactccatgaggttgcaaaatgcactggatggtactccttctgttttca--tataattat--
| |||||||||||| || ||||| ||  | ||||||||||||||||| || || || ||| ||||||||||| |||| |||||||| ||||||||||||||| |||||  |||  | ||||  ||| ||||  ||  ||||    |   |    | |     ||  |||  | | ||  ||| | |   |   || | | |   
ACCATGCTTCTGTATTTCCCATGTGGATTGATAAGAGGTGCCTTGACTAACTTAGGAATTCCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttgagctatgcttttttctgatcttt--ttaacatgtggttaattttcatcgtttggtgatctg--ttgcacatcttatatcaaccactagagtcaaac

upper sequence: LOC_Os09g06970.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 4
AGCATGCTTCTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgcactactccttttc-atgacctttactttgcatgcaactccatgaggttgcaaaatgcactggatggtactccttctgttttcatataattat--
| |||||||||||| || ||||||||| | |||||||||||||||||||| || || ||||||||||||||| |||| |||||||| ||||||||||||||| ||||   |||  | ||||| |||||||||   | |||      |   |    |      |||  |||  |  ||     | |       |  | | |   
ACCATGCTTCTGTATTTCCCATGCGGGTTGATAAGAGGTGCCTTGACCAACTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcagctatgctttttctatgaccttt---tggcacatggttaattttcatcttttgatgatctgtttcatatcttatatcaaccactggagtcaaac
















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|89170340|gb|CI039617.1|CI039617
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|88486550|gb|CI423821.1|CI423821
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|88374675|gb|CI518542.1|CI518542
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTACTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|58659704|gb|CK048384.1|CK048384
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|88442054|gb|CI560295.1|CI560295
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|8335138|gb|BE040122.1|BE040122
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAGACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|88469598|gb|CI406869.1|CI406869
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|88428061|gb|CI556955.1|CI556955
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|88506303|gb|CI433809.1|CI433809
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTT-CTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCT
EST: gi|33805948|gb|CF328853.1|CF328853
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|88508792|gb|CI436298.1|CI436298
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|66919436|gb|CX106284.1|CX106284
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|33814200|gb|CF332979.1|CF332979
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|88832250|gb|CI017484.1|CI017484
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|88510162|gb|CI437668.1|CI437668
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
EST: gi|33813782|gb|CF332777.1|CF332777
EST:     TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT                         GTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT
genomic: TTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTT

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: 72 (upstream exon), 74 (downstream exon)
Score: 21

AGCATGCTTCTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgca ... aatattgcagGTTCTTTTGTTGTGCGCATAAAAACATGAGCTGCAGATTTTATGCCTGCTTGTTCGATCAAGCGGTTTGAACATTAAAGAGTGCAAGCACGCAATAGCCT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCATGCTTCTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCGTGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATgtgagttgcactactccttttcatgacctttactttgcatgcaactccatgaggttgcaaaatgcactggatggtactccttctgttttcatataattat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc