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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttttctagactagcacctgttttgccctacatggagttcctaaattgtgtggtgatcaaaggaaaacactttcatgatttcatcatctctgatcctttattgaatctcttcttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTTGCAAGGAGCTTGGGAAACATTTGAAGATTCAAGTGATGGTCACTACTGG

Basic information

species Oryza sativa
transcript LOC_Os04g45040.2
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|58659856|gb|CK048536.1|CK048536
EST:     TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAG                         TTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
genomic: TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAGgtttttttct ... ttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
EST: gi|33675238|gb|CF303477.1|CF303477
EST:     TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAG                         TTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
genomic: TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAGgtttttttct ... ttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
EST: gi|27554371|gb|CA998271.1|CA998271
EST:     TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAG                         TTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
genomic: TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAGgtttttttct ... ttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
EST: gi|33677782|gb|CF306021.1|CF306021
EST:     GATTGATCAAGACAAAAATGCTATTCAAG                         TTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
genomic: GATTGATCAAGACAAAAATGCTATTCAAGgtttttttct ... ttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
EST: gi|58684322|gb|CK073009.1|CK073009
EST:     TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAG                         TTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
genomic: TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAGgtttttttct ... ttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
EST: gi|33676885|gb|CF305124.1|CF305124
EST:     TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAG                         TTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
genomic: TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAGgtttttttct ... ttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
EST: gi|163919907|gb|EG714909.1|EG714909
EST:     AAGACAAAAATGCTATTCAAG                         TTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
genomic: AAGACAAAAATGCTATTCAAGgtttttttct ... ttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
EST: gi|58653489|gb|CK042169.1|CK042169
EST:     TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAG                         TTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
genomic: TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAGgtttttttct ... ttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTT
EST: gi|58673974|gb|CK062660.1|CK062660
EST:     TTGTATACCCGCGCTGGACAAGATTGATCAAGACAAAAATGCTATTCAAG                         TTGTTATATTGGTTCCCA
genomic: TTGTATACCCGCGCTGGAAAAGATTGATCAAGACAAAAATGCTATTCAAGgtttttttct ... ttatattcagTTGTTATATTGGTTCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactttcatgatttcatcatctctgatcctttattgaatctcttcttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTTGCAAGGAGCTTGGGAAACATTTGAAGATTCAAGTGATGGTCACTACTGG
                    ctctgat  putative branch site (score: 4)
                                      tctcttcttatattc  putative PPT
                             tttattgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttttctagactagcacctgttttgccctacatggagttcctaaattgtgtggtgatcaaaggaaaacactttcatgatttcatcatctctgatcctttattgaatctcttcttatattcagTTGTTATATTGGTTCCCACAAGGGAATTGGCTCTACAAACATCACAAGTTTGCAAGGAGCTTGGGAAACATTTGAAGATTCAAGTGATGGTCACTACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA