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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttaagtttgtagttagactttagggtgttctattacttgcttcacttctatctgttcaaaaaggaattaatatatttgtgatgttttgctatggcagCCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGGACCTGGCAATTTGTTGTTGTTAGGCCCATATGCGCCATTCTAATGATTA

Basic information

species Oryza sativa
transcript LOC_Os07g32230.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g32230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G025242_T02 (Zea mays), 3'ss of exon 3
aacttaagtttgtagttagactttagggtgttctattactt-gcttcacttctatctgttca--aaaaggaattaatatatttgtgatgttttgctatggcagCCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGGACCTGGCAATTTGTTGTTGTTAGGCCCATATGCGCCATTCTAATGATTA
    |   |    | || |  |||| | |      || ||  | ||   |||||| | ||     ||||||| |||||   || ||  ||| || ||||||||||||||||||| ||||||||||| |||||| |||||||||||||||| |||||||||||||||||| ||||||||||  ||||  ||||||| || ||| 
--tcttcatgcacaatttgtatttaagttcacacgtttctcagtttggtttctatatctttgttgaaaggaactaataatcttatg-cgttctgttatggcagCCCCGCAATGTCCGATTGGAGCACAAAACATTGAAGCTTCTGAAGTATTGGACCTGGCAATTTGTTATTGTTAGGCCAGTATGTTCCATTCTGATTATTG
















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|115595411|gb|CT845119.1|CT845119
EST:     AGATCAAAGGGAGGGTGCTTCATCATTCCTTCTCTGTTTCCCTTTTCCTG                         CCCCGCAGTGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
genomic: AGATCAAAGGGAGGGTGCTTCATCATTCCTTCCCTGTTTCCCTTTTCCTGgtaatttcct ... gctatggcagCCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
EST: gi|33691746|gb|CF319985.1|CF319985
EST:     AGATCAAAGGGAGGGTGCTTCATCATTCCTTCCCTGTTTCCCTTTTCCTG                         CCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
genomic: AGATCAAAGGGAGGGTGCTTCATCATTCCTTCCCTGTTTCCCTTTTCCTGgtaatttcct ... gctatggcagCCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
EST: gi|33680754|gb|CF308993.1|CF308993
EST:     AGATCAAAGG-AGGGTGCTTCATCATTCCTTCCCTGTTTCCCTTTTCCTG                         CCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
genomic: AGATCAAAGGGAGGGTGCTTCATCATTCCTTCCCTGTTTCCCTTTTCCTGgtaatttcct ... gctatggcagCCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
EST: gi|38480495|gb|CF964584.1|CF964584
EST:     CATCATTCCTT-CCTGTTTCCCTTTTCCTG                         CCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
genomic: CATCATTCCTTCCCTGTTTCCCTTTTCCTGgtaatttcct ... gctatggcagCCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
EST: gi|58686677|gb|CK075364.1|CK075364
EST:     AGATCAAAGGGAGGGTGCTTCATCATTCCTTCCCTGTTTCCCTTTTCCTG                         CCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
genomic: AGATCAAAGGGAGGGTGCTTCATCATTCCTTCCCTGTTTCCCTTTTCCTGgtaatttcct ... gctatggcagCCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
EST: gi|33682368|gb|CF310607.1|CF310607
EST:     AGATCAAAGG-AGGGTGCTTCATCATTCCTTCCCTGTTTCCCTTTTCCTG                         CCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG
genomic: AGATCAAAGGGAGGGTGCTTCATCATTCCTTCCCTGTTTCCCTTTTCCTGgtaatttcct ... gctatggcagCCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttctatctgttcaaaaaggaattaatatatttgtgatgttttgctatggcagCCCCGCAATGTTCGATTGGAGCATAAAACACTGAAGCTTCTGAAGTACTGGACCTGGCAATTTGTTGTTGTTAGGCCCATATGCGCCATTCTAATGATTA
                      aattaat  putative branch site (score: 3)
                                         ttttgct  putative PPT
            ttcaaaaaggaattaa  TA-rich tract