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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGAGAGGCTAGAAGAATATCCAGGGCTTTCTGGGGTTGAGGTTTCAACCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcctatcctctgttctacacctgccacttttctgatttatacgctgagctattgcaatgctgaagcaaatggcatttacgggggcaatgcccaacgggataacaatcattccgtcttacatttcaactcaccaaatcttcaaaatactccctcattgatgtgtattttctgtttttatttctag

Basic information

species Oryza sativa
transcript LOC_Os02g47560.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47560.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G35970.1 (Arabidopsis thaliana), 5'ss of exon 6
AAGAGAGAGGCTAGAAGAATATCCAGGGCTTTCTGGGGTTGAGGTTTCAACCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgt--cctatcctctgttctacacc-tgccacttttctgatttatacgctgagctattgca-atgctgaagcaaatggcatttacgggggcaatgcccaacgggataacaatcattccgtcttacatttcaactcaccaaatcttcaaaatactccctcattgatgtgtattttctgtttttatttctag
 ||||| ||||| || || | ||||| |  |  ||| ||||||||  ||||||| || |||||||||||| |||| |||||||||||  |||| || ||||||| | |  |    | ||| ||| |  |  || ||      |  || |||     |  | | ||| ||  | ||| ||| ||   | ||      |||                                                                                                
CAGAGAAAGGCTGGATGATTTTCCAGTGGCTGATGGAGTTGAGGTCGCAACCATTGACAGCTTTCAAGGGCGGGAGGCTGATGCAGTGATCATCTCAATGgtaaacattactctgcttcttttccattctgtggcatgaagatatttcataattaaaattctagcagatagtaaag-aaacggagataacattaagaatct----------------------------------------------------------------------------------------------

upper sequence: LOC_Os02g47560.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv16s0039g00520.t01 (Vitis vinifera), 5'ss of exon 6
AAGAGAGAGGCTAGAAGAATATCCAGGGCTTTCTGGGGTTGAGGTTTCAACCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcctatcctctgttc-tacacctgccacttttctgatttatacgctgagctattgcaatgctgaagcaaatggcatttacgggggcaatgcccaacgggataacaatcattccgtcttacatttcaactcaccaaatcttcaaaatactccctcattgatgtgtattttctgtttttatttctag
 ||||| ||||| || ||   |||||    |   || ||||||||| |||| || ||||||||||||||  |||| |||||||||||| | ||||| |||||| || || |||| |   | | |  ||    ||  ||| |||  |     ||| | ||   ||   |   |  || |     ||  |||     ||||| ||                                                                                         
GAGAGACAGGCTTGATGAGATTCCAGAAGCTGTAGGTGTTGAGGTTGCAACTATTGATAGCTTTCAAGGCCGGGAGGCTGATGCAGTTATTATATCAATGgtatgcctcttatctttattacatgaacacttcaaatttgtgaagtgc---ctgggttag-acatgacatgacaaagttttggttgagggatatgtgcccgaca----------------------------------------------------------------------------------------
















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|88669550|gb|CI723214.1|CI723214
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88676395|gb|CI730508.1|CI730508
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88665622|gb|CI715778.1|CI715778
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|89172152|gb|CI721211.1|CI721211
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88668007|gb|CI722746.1|CI722746
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88669799|gb|CI723915.1|CI723915
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88671306|gb|CI724352.1|CI724352
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88671068|gb|CI725184.1|CI725184
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88668823|gb|CI719780.1|CI719780
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88676987|gb|CI731100.1|CI731100
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88593507|gb|CI713461.1|CI713461
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88677056|gb|CI731169.1|CI731169
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88671100|gb|CI725216.1|CI725216
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88671307|gb|CI724353.1|CI724353
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88665896|gb|CI716052.1|CI716052
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88677001|gb|CI731114.1|CI731114
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88671823|gb|CI725358.1|CI725358
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88908969|gb|CI716693.1|CI716693
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88674583|gb|CI728696.1|CI728696
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88675511|gb|CI729624.1|CI729624
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88671692|gb|CI725723.1|CI725723
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88594617|gb|CI714575.1|CI714575
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88666399|gb|CI716555.1|CI716555
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCANTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88669680|gb|CI723796.1|CI723796
EST:     NCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: -CATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88671687|gb|CI725718.1|CI725718
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88670865|gb|CI724981.1|CI724981
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
EST: gi|88669895|gb|CI724011.1|CI724011
EST:     CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATG                         GTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC
genomic: CCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGC

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: 63 (upstream exon), 57 (downstream exon)
Score: 12

AAGAGAGAGGCTAGAAGAATATCCAGGGCTTTCTGGGGTTGAGGTTTCAACCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcc ... ttatttctagGTTCGATCAAACCCACTGGGAGCGGTAGGTTTCCTTGGTGACAGCAGGCGCATGAATGTGGCTATTACAAGGGCATGCCGGCATGTCACCGTGGTATGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAGAGAGGCTAGAAGAATATCCAGGGCTTTCTGGGGTTGAGGTTTCAACCATAGATAGCTTTCAAGGGAGGGAAGCTGATGCAGTTGTCATATCGATGgtaagcgtcctatcctctgttctacacctgccacttttctgatttatacgctgagctattgcaatgctgaagcaaatggcatttacgggggcaatgcccaacgggataacaatcattccgtcttacatttcaactcaccaaatcttcaaaatactccctcattgatgtgtattttctgtttttatttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT