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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGATGCCATTTCTCGAGCAACAACAATTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagctcaggctgatacatttactcactacaaagaaaaaaaaagaatcttaatttcaccgtactcatttttcctag

Basic information

species Oryza sativa
transcript LOC_Os10g25130.1
intron # 6
splice site 5'
intron type U2

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|25799461|gb|CA755422.1|CA755422
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCANTTGCTGCTGGAATTGCATCACGTGAC
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|88361410|gb|CI605191.1|CI605191
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|29667022|gb|CB663297.1|CB663297
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|2428328|gb|C72791.1|C72791
EST:     TCTTGCCTCGATTCCTGGAAGAGCA-CTGGAGCATACAGCCACAGC-ANG                         GGCATCAANGG-CTCCCTGATGNA-TTGCTGCTG
genomic: TCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCA-Ggtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTG
EST: gi|29665582|gb|CB661857.1|CB661857
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|14191907|gb|AU184118.1|AU184118
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCAAT
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAAT
EST: gi|157652418|gb|EX452052.1|EX452052
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GACATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAT
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|157652409|gb|EX452043.1|EX452043
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAT
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|58691201|gb|CK079888.1|CK079888
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         CGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAT
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|86850230|gb|CI305469.1|CI305469
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|157652426|gb|EX452060.1|EX452060
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATACAATTGCTGCTGGAATTGCATCACGTGAT
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|88412291|gb|CI573567.1|CI573567
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|27553989|gb|CA997889.1|CA997889
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
EST: gi|33675102|gb|CF303341.1|CF303341
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGA
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGG-CTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGA
EST: gi|33691675|gb|CF319914.1|CF319914
EST:     TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAG                         GGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC
genomic: TTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGAC

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: 75 (upstream exon), 75 (downstream exon)
Score: 121

TGCTGATGCCATTTCTCGAGCAACAACAATTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagct ... tttttcctagGGCATCAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGACGGATACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGATGCCATTTCTCGAGCAACAACAATTCTTGCCTCGATTCCTGGAAGAGCAACTGGAGCATACAGCCACAGCCAGgtgagcagctcaggctgatacatttactcactacaaagaaaaaaaaagaatcttaatttcaccgtactcatttttcctag

- - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA