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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagacctatcaaaaggaaacttattacaatattctgtcagcagtagaatatccagtggaaactagaacaccaattcctgctcgcatcacagtggttatgttggagttatatataataagaaattgcgcattaccctttttgaccatacctttcatatgctttacagGTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGTATCTTCGCTTGGTGTTCAGTGGGAGGATGTATATAAAACCGTCGAAAAT

Basic information

species Oryza sativa
transcript LOC_Os01g65780.1
intron # 3
splice site 3'
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|58677045|gb|CK065732.1|CK065732
EST:     CATCTGTGTACGACCATC-AATGCAGTCTAG-TCTCG                         G-TTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGT
genomic: CATCTGTGTACGACCATCAAATGCAGTCTAGTTCTCGgtgagtagac ... tgctttacagGTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGT
EST: gi|88417885|gb|CI596562.1|CI596562
EST:     CTATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGTTCTCG                         GTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGT
genomic: CTATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGTTCTCGgtgagtagac ... tgctttacagGTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGT
EST: gi|33796413|gb|CF324073.1|CF324073
EST:     TATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGTTTCTCG                         GTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATG
genomic: TATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGTT-CTCGgtgagtagac ... tgctttacagGTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATG
EST: gi|29630115|gb|CB635124.1|CB635124
EST:     CTATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGTTCTCG                         GTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGT
genomic: CTATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGTTCTCGgtgagtagac ... tgctttacagGTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGT
EST: gi|33794578|gb|CF323176.1|CF323176
EST:     TATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGNNTCTCG                         GTTTGTCAGTGGGTGGGATATGGGACAAGACCATTCCTGATCCACGATAT
genomic: TATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGT-TCTCGgtgagtagac ... tgctttacagGTTTGTCAGTGGGTGG-ATATGGGACAAGACCATTCCTGATCCACGATAT
EST: gi|13420432|gb|AU174522.1|AU174522
EST:     CTATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGTTCTCG                         GTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGT
genomic: CTATTGTACACTCCATCTGTGTACGACCATCAAATGCAGTCTAGTTCTCGgtgagtagac ... tgctttacagGTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataataagaaattgcgcattaccctttttgaccatacctttcatatgctttacagGTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGTATCTTCGCTTGGTGTTCAGTGGGAGGATGTATATAAAACCGTCGAAAAT
                         ttttgac  putative branch site (score: 3)
     aagaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagacctatcaaaaggaaacttattacaatattctgtcagcagtagaatatccagtggaaactagaacaccaattcctgctcgcatcacagtggttatgttggagttatatataataagaaattgcgcattaccctttttgaccatacctttcatatgctttacagGTTTGTCAGTGGGTGGATATGGGACAAGACCATTCCTGATCCACGATATGTATCTTCGCTTGGTGTTCAGTGGGAGGATGTATATAAAACCGTCGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG