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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatatgttaatggagggagtatatcaattattgtgtgtggatatttatctcatttggaacaagtcatcattatttttaattactctgtacatttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATAGTGCCAAAGCAATCAAAGTTAGATGGAGAAGATTCAGTGTTTCAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g46510.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM5G824843_T01 (Zea mays), 3'ss of exon 3
acatatgttaatggagggagtatatcaattattgtgtgtgg----atatttatctcatttggaacaagtcatcattatttttaattactctgtacatttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATAGTGCCAAAGCAATCAAAGTTAGATGGAGAAGATTCAGTGTTTCAGAAAG
   | ||  |||   |  | |||||  | |  |||   |      ||||||||     ||  |   |    | ||| || |||  | ||       | |  ||||||||||| ||||||||||||||||| |||||||| ||||| ||||||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||
---tctggcaatct-gttaatatattgaatgatgtacatattgacatatttattgttcttacattgacattttattgttcttacatccttcacttctgttccagGTTGTTCGTTTAGCCTCCTTTCAGTACGCTCCATCGATACCACCATTTATAGTACCAAAGCAATCCAAGTTCGATGGAGATGATTCAGTGTTTCAGAAAG
















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|88352827|gb|CI678852.1|CI678852
EST:     CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAG                         GTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
genomic: CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAGgtacagtttt ... catttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
EST: gi|58666107|gb|CK054793.1|CK054793
EST:     CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAG                         GTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
genomic: CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAGgtacagtttt ... catttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
EST: gi|88585007|gb|CI702607.1|CI702607
EST:     CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAG                         GTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
genomic: CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAGgtacagtttt ... catttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
EST: gi|58665271|gb|CK053957.1|CK053957
EST:     CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAG                         GTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
genomic: CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAGgtacagtttt ... catttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
EST: gi|58587152|gb|CF985460.1|CF985460
EST:     CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAG                         GTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
genomic: CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAGgtacagtttt ... catttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
EST: gi|88852155|gb|CI683673.1|CI683673
EST:     CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAG                         GTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
genomic: CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAGgtacagtttt ... catttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
EST: gi|58612142|gb|CK039854.1|CK039854
EST:     CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAG                         GTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
genomic: CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAGgtacagtttt ... catttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
EST: gi|58662716|gb|CK051402.1|CK051402
EST:     CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAG                         GTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
genomic: CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAGgtacagtttt ... catttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
EST: gi|58669479|gb|CK058165.1|CK058165
EST:     CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAG                         GTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA
genomic: CCAAGACTACCACTTCTGAGAAAATAGCTTTAAGACCTCCAATGTTGCAGgtacagtttt ... catttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctcatttggaacaagtcatcattatttttaattactctgtacatttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATAGTGCCAAAGCAATCAAAGTTAGATGGAGAAGATTCAGTGTTTCAGAAAG
                             ttttaat  putative branch site (score: 3)
                                             catttctc  putative PPT
                aagtcatcattatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatatgttaatggagggagtatatcaattattgtgtgtggatatttatctcatttggaacaagtcatcattatttttaattactctgtacatttctcagGTTGTTCGGTTAGCCTCCTTTCAGTATGCTCCATCTATACCCCCATTTATAGTGCCAAAGCAATCAAAGTTAGATGGAGAAGATTCAGTGTTTCAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
-catatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaag