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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCAGGCGGGCCGCGTATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaagccgcctaggatcaccattttcagcacacaccagtttgttgggtaattgcagcataattgcagcattttatttgctatgaagtgtccttcg...

Basic information

species Oryza sativa
transcript LOC_Os02g52420.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 2
GAAGCAGGCGGGCCGCGTATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaagccgcctaggatcaccattttcagcacacaccagtttgttgggtaattgcagcataattgcagcattttatttgctatgaagtgtccttcg------------
| |||||||||   |||||||| || ||||||||||| |||||| ||||||||||||| || |||||  |||   |||    ||   ||  ||| || |   |   || ||||||||  ||| | | | |    | || ||| | |  |||| ||  |||| | ||             
GCAGCAGGCGGCTGGCGTATCAAGCAACGAGAACGCTATGCAACTTGGTGGATATCCTATTTAACAG--GAGgtgagc--tttaacttcgtcatatttactgct--cctgtttgttgcataactactgtag---tacaccatctaagctgctctgtggtgttcctcctcctgggcatgt
















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|88501858|gb|CI696987.1|CI696987
EST:     TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAG                         AGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
genomic: TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
EST: gi|88401127|gb|CI685112.1|CI685112
EST:     TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAG                         AGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
genomic: TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
EST: gi|88368945|gb|CI675673.1|CI675673
EST:     TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAG                         AGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
genomic: TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
EST: gi|88453699|gb|CI683955.1|CI683955
EST:     TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAG                         AGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
genomic: TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
EST: gi|88730684|gb|CI754297.1|CI754297
EST:     TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAG                         AGGTCAGAGTGACAAACCGGAAGATAACCCTAGAAGCCTACGGCCTGCGAA
genomic: TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
EST: gi|88501800|gb|CI695558.1|CI695558
EST:     TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAG                         AGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
genomic: TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
EST: gi|88664392|gb|CI688470.1|CI688470
EST:     TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAG                         AGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
genomic: TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
EST: gi|29657569|gb|CB653844.1|CB653844
EST:     TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAG                         AGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
genomic: TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
EST: gi|88664755|gb|CI702439.1|CI702439
EST:     TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAG                         AGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA
genomic: TATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAA

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: 48 (upstream exon), 55 (downstream exon)
Score: 16

GAAGCAGGCGGGCCGCGTATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaag ... aatcttgcagAGGTCAGAGTGACAAACCGGAAGATAACCCTAGACGCCTACGGCCTGGGAAAGTATCTCCTCGTCTAAGCGTTCCCAAACATATACAGCGGCCACCATAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCAGGCGGGCCGCGTATCAGGCGACGAGAACGCTCTGCAACCTGGTGGATATCCTCTTCAACAGgtgagccaagccgcctaggatcaccattttcagcacacaccagtttgttgggtaattgcagcataattgcagcattttatttgctatgaagtgtccttcg

- - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - GGTGGA