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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAGCCCGCCGAGACGATCTCCTCCGCCGAGCAGCGCCGATCTCCCCTCCCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatccccgtacgtacgcgcatccccttcctcatccctctccacccacgccttctctctacgcggctatgccttaacccttagcttctccttctag...

Basic information

species Oryza sativa
transcript LOC_Os08g36994.2
intron # 1
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|88426936|gb|CI601897.1|CI601897
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88432599|gb|CI567638.1|CI567638
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88298560|gb|CI563555.1|CI563555
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88423107|gb|CI613408.1|CI613408
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         GTTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88717019|gb|CI740529.1|CI740529
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88407200|gb|CI581287.1|CI581287
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|117227378|gb|CT846566.1|CT846566
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88350670|gb|CI617525.1|CI617525
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88718278|gb|CI741367.1|CI741367
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88403432|gb|CI573155.1|CI573155
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88346534|gb|CI622991.1|CI622991
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88399316|gb|CI618506.1|CI618506
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         GTTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88422593|gb|CI571575.1|CI571575
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88573870|gb|CI665639.1|CI665639
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88392450|gb|CI612924.1|CI612924
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88415381|gb|CI586587.1|CI586587
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88316708|gb|CI624150.1|CI624150
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88311485|gb|CI572541.1|CI572541
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88398641|gb|CI598606.1|CI598606
EST:     CCGCGAGCANNNNNNNCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88402931|gb|CI568705.1|CI568705
EST:     CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88362823|gb|CI614179.1|CI614179
EST:     CCGCGAGCAGCGGGGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCG                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: CCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG

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: 35 (upstream exon), 74 (downstream exon)
Score: 4

AGGAGCCCGCCGAGACGATCTCCTCCGCCGAGCAGCGCCGATCTCCCCTCCCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatcc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAGACACTATAGTTAGGGGCTTAGAGTAACCTGGTTACAGATAATGTCTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAGCCCGCCGAGACGATCTCCTCCGCCGAGCAGCGCCGATCTCCCCTCCCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGgtgagcatccccgtacgtacgcgcatccccttcctcatccctctccacccacgccttctctctacgcggctatgccttaacccttagcttctccttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc