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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttcaattatcttaacatatctgtaaataagtgttcaagttgagatatatagtcccacttatatcttgcaccgcttgttctggtgttttgtaatttttgttttatatggaggggtaacacatcatattttgtatctag

Basic information

species Oryza sativa
transcript LOC_Os05g19954.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g19954.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G095782_T04 (Zea mays), 5'ss of exon 3
TGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttcaattatctta--acatatctgtaaataagtgttcaagttgagatatatagtcccactta--tatcttgcaccgcttgttctggtgttttgtaatttttgttttatatggaggggtaacacatcatattt--tgtatctag
     | | ||| ||||||| | | ||||||| ||||||||||| ||| | || ||||| || || || ||||| || |||||||||||||||||||||||||||||| ||| | | ||   |||| ||||| |     | | || |||| || |||  ||    ||   |||| ||||| | |   | |    | || |  ||| | |   |||  | ||| | ||| |  ||||||  ||| |  ||
-----TCTAGAGGATGCGCTGATATGCATCACTAAGCTGGATCGGAAGAAACTATGCTTAGTCGGTGCAGGCAGGACTGATACAGGTGTTCATGCATGGGGTCAGgtttaataaacatactgcataactgtatactgaagcttaaattgatatctatcatctggtttgcgtatcctgcactgttaaatgtca-atattatgttttatatgaaatactgggggattacatacaatatttgttgttttcag

upper sequence: LOC_Os05g19954.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G095782_T05 (Zea mays), 5'ss of exon 3
---------------TGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttcaattatctta--acatatctgtaaataagtgttcaagttgagatatatagtcccactta--tatcttgcaccgcttgttctggtgttttgtaatttttgttttatatggaggggtaacacatcatattt--tgtatctag
               | |  | | ||| ||||||| | | ||||||| ||||||||||| ||| | || ||||| || || || ||||| || |||||||||||||||||||||||||||||| ||| | | ||   |||| ||||| |     | | || |||| || |||  ||    ||   |||| ||||| | |   | |    | || |  ||| | |   |||  | ||| | ||| |  ||||||  ||| |  ||
ATTCCAACAATACAATATTTTCTAGAGGATGCGCTGATATGCATCACTAAGCTGGATCGGAAGAAACTATGCTTAGTCGGTGCAGGCAGGACTGATACAGgtgttcatgcatggggtcaggtttaataaacatactgcataactgtatactgaagcttaaattgatatctatcatctggtttgcgtatcctgcactgttaaatgtca-atattatgttttatatgaaatactgggggattacatacaatatttgttgttttcag

upper sequence: LOC_Os05g19954.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G095782_T01 (Zea mays), 5'ss of exon 2
TGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttcaattatctta--acatatctgtaaataagtgttcaagttgagatatatagtcccactta--tatcttgcaccgcttgttctggtgttttgtaatttttgttttatatggaggggtaacacatcatattt--tgtatctag
| |  | | ||| ||||||| | | ||||||| ||||||||||| ||| | || ||||| || || || ||||| || |||||||||||||||||||||||||||||| ||| | | ||   |||| ||||| |     | | || |||| || |||  ||    ||   |||| ||||| | |   | |    | || |  ||| | |   |||  | ||| | ||| |  ||||||  ||| |  ||
TATTTTCTAGAGGATGCGCTGATATGCATCACTAAGCTGGATCGGAAGAAACTATGCTTAGTCGGTGCAGGCAGGACTGATACAGGTGTTCATGCATGGGgtcaggtttaataaacatactgcataactgtatactgaagcttaaattgatatctatcatctggtttgcgtatcctgcactgttaaatgtca-atattatgttttatatgaaatactgggggattacatacaatatttgttgttttcag

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|88570006|gb|CI661181.1|CI661181
EST:     GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGG                         GTCAGGTGGCGCATTTCACCACGCCTTTTTCCTACCATTGTCTTGATAGCA
genomic: GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttca ... ttgtatctagGT--GG---CGCATTTCACCACGCCTTTTTCCTACCATTGTCTTGATAGCA
EST: gi|88691366|gb|CI733949.1|CI733949
EST:     GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGG                         GTGGCGCATTTCACCACG
genomic: GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttca ... ttgtatctagGTGGCGCATTTCACCACG
EST: gi|88689634|gb|CI733210.1|CI733210
EST:     GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGG                         GTGGCGCATTTCACCACGCCTTTTTCCTACCATTGTCTTGATAGCATG
genomic: GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttca ... ttgtatctagGTGGCGCATTTCACCACGCCTTTTTCCTACCATTGTCTTGATAGCATG
EST: gi|33807142|gb|CF329453.1|CF329453
EST:     GCTCTGCTCGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGG                         GCGGCGCATTTCACCACGCCTTTTTCCTACCATTGTCTTGATAGCATGCAC
genomic: GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttca ... ttgtatctagGTGGCGCATTTCACCACGCCTTTTTCCTACCATTGTCTTGATAGCATGCAC
EST: gi|88689372|gb|CI732948.1|CI732948
EST:     GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGG                         GTGGCGCATTTCACCACGCCTTTTTCCTACCATTGTCTTGATAGCATG
genomic: GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttca ... ttgtatctagGTGGCGCATTTCACCACGCCTTTTTCCTACCATTGTCTTGATAGCATG
EST: gi|88691736|gb|CI733814.1|CI733814
EST:     GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGG                         GTGGCGCATTTCACCACG
genomic: GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttca ... ttgtatctagGTGGCGCATTTCACCACG
EST: gi|88332716|gb|CI660234.1|CI660234
EST:     GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGG                         GTCAGGTGGCGCATTTCACCACGCCTTTTTCCTACCATT
genomic: GCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttca ... ttgtatctagGT--GG---CGCATTTCACCACGCCTTTTTCCTACCATT

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: 61 (upstream exon), 49 (downstream exon)
Score: 4

TGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttca ... ttgtatctagGTGGCGCATTTCACCACGCCTTTTTCCTACCATTGTCTTGATAGCATGCACTCTGCAATCAATGGGCTTCTTCCACATGAGATTCGAGTGAGGGAAATTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGGAGCTGGCAGAACAGATACAGGTGTTCATGCATGGGgtcaggttcaattatcttaacatatctgtaaataagtgttcaagttgagatatatagtcccacttatatcttgcaccgcttgttctggtgttttgtaatttttgttttatatggaggggtaacacatcatattttgtatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT