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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagatttttgcatacctgaaatttctgcagtttgtcttctttttaacataccacaaactggagctatatccgcatcatattgagcatttatcctcagtttaattggttctttttccctttttctgctgccagGTCAACTGCGTTGTCATGCGTGGAATGAATGATGACGAGATCTGTGATTTTGTTGAAATGACGAGAGACAAGCCTGTCAATGTCAGATTTATAGAGTTTA

Basic information

species Oryza sativa
transcript LOC_Os02g15870.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15870.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G135816_T01 (Zea mays), 3'ss of exon 2
gtatgcagatttttgcatacctgaaatttctgcagtt-tgtcttctttttaacataccacaaactggagctatatccgcatcatattgagcattta-tcctcagttt-aattggttctttttccctttttctgctg---ccagGTCAACTGCGTTGTCATGCGTGGAATGAATGATGACGAGATCTGTGATTTTGTTGAAATGACGAGAGACAAGCCTGTCAATGTCAGATTTATAGAGTTTA
||||  || ||||||||| | |  || |  |||| || | |    |        | |   |   ||||   |||| |   ||| | ||| ||| || |  | |||||  ||   || ||||| ||   |||| ||    |||||||||||| ||  |||||||||| || |||||||| ||||||||  ||||||||||| |||||||| |||||||  |||| || |||||||| |||||||
gtatctagttttttgcatgc-tacaactcatgcaattctattaagtcaactgttttctctatgatggaaacatattc---tcaaaatgaacatctagtatttagttttgatcaattatttttgcccacttcttctatacccagGTCAACTGTGTCATCATGCGTGGTATAAATGATGATGAGATCTGCAATTTTGTTGAATTGACGAGACACAAGCCCATCAACGTTAGATTTATTGAGTTTA

upper sequence: LOC_Os02g15870.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G31955.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcagatttttgcatacctgaaatttctgcagtttgtcttctttttaacataccacaaactggagctatatccgcatcatattgagcatttatcctcagtttaattggttctttttccctttttctgctgccagGTCAACTGCGTTGTCATGCGTGGAATGAATGATGACGAGATCTGTGATTTTGTTGAAATGACGAGAGACAAGCCTGTCAATGTCAGATTTATAGAGTTTA
              | ||   |   | | || |    ||| |||| ||| |      |   |   || | ||||  |    || || |  | || |      |  || | ||||||  |            || |||||||| || ||| ||||| | ||| |||||||||| ||||| ||||||||||||||  ||||  | ||||||||  |||||||| | || || |||||||
--------------gtatgtttattaatccttcttcatgttttctgtttga------atgtagcagaacgatatttg----atgttcaagagtttt------tgcaaatcgttcttggttt----------tgacagGTCAATTGTGTTATCATGAGGGGATTGAATGATGATGAGATTTGTGATTTTGTTGAGTTGACACGCGACAAGCCAATCAATGTCCGGTTCATCGAGTTTA

upper sequence: LOC_Os02g15870.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------gtatgcagatttttgc--atacctgaaatttctg-cagtttgtcttctttttaacataccacaaactggagctatatccgcatcat--attgagcatt-tatcctcagtttaat---tggttctttttccctttttctgc------tgccagGTCAACTGCGTTGTCATGCGTGGAATGAATGATGACGAGATCTGTGATTTTGTTGAAATGACGAGAGACAAGCCTGTCAATGTCAGATTTATAGAGTTTA
                            | ||||   |  ||||  | | |||   |||  |  ||||| ||||  |   ||  ||  |  |  |     |   |  |  | ||  ||||    || ||     || ||||    |  ||   || |  |  |||||       |  ||||| ||||| ||||| ||||||||  | |||||||| |||||||||||||| || || |||||  | || || ||  | ||| |  | ||||| ||||| |
gtatgttttgtcttttcaatttatgattgcatgcctttccttgctaaaatctgttcttttagatagtttctctttctgccaaagtaatattaggtcttattcattaggtcttattcattgtcttttataatgcaagattaaaacatattttccttccattcattctgtacgctgtctcagGTGAACTGTGTTGTAATGCGTGGGTTCAATGATGATGAGATCTGTGATTTCGTAGAGATGACTCGTGATAAACCAATTAATATTCGGTTTATTGAGTTCA

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|33654217|gb|CF276831.1|CF276831
EST:     TCATGGAATCGATAGATGCTTCTATACAACTTGGATTCCAATCTGTCAAG                         GTCAACTGCGTTGTCATGCGTGGAATGAATGATGACGAGATCTGTGATTTT
genomic: TCATGGAATCGATAGATGCTTCTATACAACTTGGATTCCAATCTGTCAAGgtatgcagat ... ctgctgccagGTCAACTGCGTTGTCATGCGTGGAATGAATGATGACGAGATCTGTGATTTT
EST: gi|29675363|gb|CB671638.1|CB671638
EST:     CATGGAATCGATAGATGCTTCTATACAACTTGGGATTCCAATCTGTCAAG                         GTCNACTGCGTTGTCATGCGTGGAATGAATGAT
genomic: CATGGAATCGATAGATGCTTCTATACAACTTGG-ATTCCAATCTGTCAAGgtatgcagat ... ctgctgccagGTCAACTGCGTTGTCATGCGTGGAATGAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgagcatttatcctcagtttaattggttctttttccctttttctgctgccagGTCAACTGCGTTGTCATGCGTGGAATGAATGATGACGAGATCTGTGATTTTGTTGAAATGACGAGAGACAAGCCTGTCAATGTCAGATTTATAGAGTTTA
                   gtttaat  putative branch site (score: 4)
                         ttggttctttttccct  CT-rich tract
                  agtttaatt  TA-rich tract