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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcatgtactgtgattatattgatggatccgatatcttgtgatcgatgcttgaaatgatttggtgaacgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATGGATGAGTGAATCCCCCAGCCTAATCATA

Basic information

species Oryza sativa
transcript LOC_Os03g21140.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21140.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 7
gtatg---gcatgtactgtgattatattgatggatccgatatcttgtgatcgatgcttgaaatgat----ttggtgaacgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATGGATGAGTGA-ATCCCCCAGCCTAATCATA
|| ||   || | |||| |   | |   | ||      || ||| || ||| | |  ||||   ||    |   |||| ||||| ||||||||| |||| ||||||||||| || |||||||||||||| |     | |  |||| | | |||||| ||||||||||
gtttgttcgcctctactttcggtgtggcggtgcggattatgtct-gtcatccacgaatgaagaaataatgtctctgaatgcaatgagcagGCTGTCCTCCGATCACGGAGCCATGGGGATGTAAAGTTCACCATTGTAGGCGAGTTATACCCCCCAACCTAATCATA

upper sequence: LOC_Os03g21140.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G003424_T01 (Zea mays), 3'ss of exon 7
-------------------gtatggca-tgtactgtgattatattgatggatccga-tatcttgtgatcgatgcttgaaatgatttggt--gaacgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATGGATGAGTGAATCCCCCAGCCTAATCATA
                    ||    | | | | |||       | |||     ||  ||  ||| ||| | |  ||||||||||   |  ||||||||| ||||||||| |||| ||||||||||| || ||||||||||||||            |||||| | ||||||||||||||||
gtgcgttggaaaggcctctctactctacttttccgtggcgccgattatgtccgtgaacattctgtcatccacgagtgaaatgattctctccgaacgcaatgagcagGCTGTCCTCCGATCACGGAGCCATGGGGATGTAAAGTTCAGCATTGGAAGCGAGTGA-TACCCCAGCCTAATCATA

upper sequence: LOC_Os03g21140.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G003424_T04 (Zea mays), 3'ss of exon 5
-------------------gtatggca-tgtactgtgattatattgatggatccga-tatcttgtgatcgatgcttgaaatgatttggt--gaacgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATGGATGAGTGAATCCCCCAGCCTAATCATA-------------------------
                    ||    | | | | |||       | |||     ||  ||  ||| ||| | |  ||||||||||   |  ||||||||| ||||||||| |||| ||||||||||| || ||||||||||||||            |||||| | ||||||||||||||||                         
gtgcgttggaaaggcctctctactctacttttccgtggcgccgattatgtccgtgaacattctgtcatccacgagtgaaatgattctctccgaacgcaatgagcagGCTGTCCTCCGATCACGGAGCCATGGGGATGTAAAGTTCAGCATTGGAAGCGAGTGA-TACCCCAGCCTAATCATAGTAAGCACTAACGTCCCTCTTTATT

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|32948198|gb|BP184770.1|BP184770
EST:     CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAG                         --G-CTGGCCTCTGATCACGGAGCGATTGGGATGTAA
genomic: CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAGgtatggcatg ... acgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAA
EST: gi|58659366|gb|CK048046.1|CK048046
EST:     CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAG                         --G-CTGGCCTCTGATCACGGAGCGATTGGGATGTAAA
genomic: CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAGgtatggcatg ... acgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAA
EST: gi|86494717|gb|CI137350.1|CI137350
EST:     CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAG                         --G-CTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
genomic: CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAGgtatggcatg ... acgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
EST: gi|58664822|gb|CK053508.1|CK053508
EST:     CCCTCTACTTTGG--ATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAG                         CAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
genomic: CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAGgtatggcatg ... acgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
EST: gi|86480759|gb|CI123392.1|CI123392
EST:     CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAG                         --G-CTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
genomic: CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAGgtatggcatg ... acgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
EST: gi|163925986|gb|EG712314.1|EG712314
EST:     CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAG                         --G-CTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
genomic: CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAGgtatggcatg ... acgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
EST: gi|88960042|gb|CI381920.1|CI381920
EST:     CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTT-C--                         CAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
genomic: CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAGgtatggcatg ... acgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
EST: gi|218490471|gb|FG964032.1|FG964032
EST:     CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAG                         --G-CTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG
genomic: CCCTCTACTTTGGATATACCTTCGCCAAGAGACTTCTTCTCGGTTTCCAGgtatggcatg ... acgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggatccgatatcttgtgatcgatgcttgaaatgatttggtgaacgcaataagCAGGCTGGCCTCTGATCACGGAGCGATTGGGATGTAAAGTTCTCTGCAATGGATGAGTGAATCCCCCAGCCTAATCATA
 tattgat  putative branch site (score: 3)
                               aaatgattt  TA-rich tract