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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctattggttccatttctacggtttccttttcttttagttttgtggcaagcatatcctagcaattttacttaaccattttcctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGATTCCGCTGTGATGCTTTCTGTTAGCAAAGAAGTTCCATGGTACCTG

Basic information

species Oryza sativa
transcript LOC_Os07g45350.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G020574_T04 (Zea mays), 3'ss of exon 3
gtatctattggttccatttctacggtttccttttcttttagt------tttgtggcaagc-atatcctagc---aattttacttaaccattttcctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGATTCCGCTGTGATGCTTTCTGTTAGCAAAGAAGTTCCATGGTACCTG----
||| ||| || || ||||       |||  | || ||    |      | ||  ||||    |||| ||     | || | ||| |  | |||| | | ||||||||| ||||||||||| |||||||| ||||| ||||| |||||||||||||| || ||||||||||||||||||||||| ||||||||||| |||    
gtaactactgatttcattctcttttttttttgttattacgatgggtagtgtgctgcaatttgtatcttatttttatttctgcttga--actttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTGGTAA

upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 3
gtatctattggttccatttctacggtttccttttcttttagt------tttgtggcaagc-atatcctagc---aattttacttaaccattttcctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGATTCCGCTGTGATGCTTTCTGTTAGCAAAGAAGTTCCATGGTACCTG
||| ||| || || ||||       |||  | || ||    |      | ||  ||||    |||| ||     | || | ||| |  | |||| | | ||||||||| ||||||||||| |||||||| ||||| ||||| |||||||||||||| || ||||||||||||||||||||||| ||||||||||| |||
gtaactactgatttcattctcttttttttttgttattacgatgggtagtgtgctgcaatttgtatcttatttttatttctgcttga--actttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG

upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 3
gtatctattggttccatttctacggtttccttttcttttagttttgtggcaagcatatcctagcaatttta------cttaaccattttcctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGATTCCGCTGTGATGCTTTCTGTTAGCAAAGAAGTTCCATGGTACCTG
||| ||| || || ||||  |    ||   |||    |  ||  ||||       ||   ||| | || ||      ||||| |||| || |    |||||||||||||||||| | |||||||||||||||||||| |||||||||||||| || || |||||||||||||||||||| ||||||||||| |||
gtaactactgatttcattcatcattttgtttttatgatgggtaatgtgatgcaattaatttagtatttctatttctgcttaaacattctctttc--tagGCAGAACAACACTTCTTGAAGCACAACGATGCTGGATCCTGGATTCAAGATTCTGCAGTTATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG

upper sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G02920.1 (Glycine max), 3'ss of exon 3
---------------gtatctattggttccatttctacggtttccttttcttttagttttgtggcaagcatatcctagcaattttacttaaccattttcctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGATTCCGCTGTGATGCTTTCTGTTAGCAAAGAAGTTCCATGGTACCTG
               | | ||| |   |||||||     |  |  |  |  | |  | ||   |     || |  ||   |   |  |  |  |||||||| |  |||||||| ||||| || || || ||||| |||||||| || ||||| |||||||||||| ||||||| ||  | || ||||| ||||| ||||| |||
gtacgtagacataaagca-ctaatatctccattttacgaggatgttgcttatgtcatcttaccgttgtgat-taatattgaacctcatctataattttccttt--tagGCAGAGCAACATTTTCTTAAACACAATGATGCTGGTTCCTGGATACAAGATTCCGCTTTGATGCTATCAATGAGTAAAGAGGTTCCTTGGTATCTG

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|58695660|gb|CK084347.1|CK084347
EST:     CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACG                         GCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
genomic: CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACGgtatctattg ... cctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
EST: gi|29684518|gb|CB680793.1|CB680793
EST:     CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACG                         GCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
genomic: CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACGgtatctattg ... cctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
EST: gi|58693123|gb|CK081810.1|CK081810
EST:     CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACG                         GCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
genomic: CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACGgtatctattg ... cctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
EST: gi|29680615|gb|CB676890.1|CB676890
EST:     CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACG                         GCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
genomic: CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACGgtatctattg ... cctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
EST: gi|88299031|gb|CI568034.1|CI568034
EST:     CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACG                         GCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
genomic: CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACGgtatctattg ... cctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
EST: gi|66923542|gb|CX110390.1|CX110390
EST:     CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACG                         GCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT
genomic: CACTTATCTGCCAACAAAGTGGCATGAGAGGTGTAATAGTAGAGGAAACGgtatctattg ... cctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttttgtggcaagcatatcctagcaattttacttaaccattttcctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGATTCCGCTGTGATGCTTTCTGTTAGCAAAGAAGTTCCATGGTACCTG
                                acttaac  putative branch site (score: 3)
                                      ccattttcctct  CT-rich tract
                          aattttacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctattggttccatttctacggtttccttttcttttagttttgtggcaagcatatcctagcaattttacttaaccattttcctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGATTCCGCTGTGATGCTTTCTGTTAGCAAAGAAGTTCCATGGTACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT