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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcaagaaaatgaaaagagaagatttttatgtatcttaatcgtattccttgtgcttgatgtagcccccttttgcatttgctcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAGAAGCTCTTGCAAGAGGCCTACAAGAGGGAGAGCAGTGACAACATAACTT

Basic information

species Oryza sativa
transcript LOC_Os04g56450.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 7
gtaaattcaagaaaatgaaa----ag----agaagatttttatgtatcttaatcgtattccttgtgcttgatg---tag--cccccttttgcatttgctctt-------------atgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAGAAGCTCTTGCAAGAGGCCTACAAGAGGGAGAGCAGTGACAACATAACTT
|||| ||    ||   | |     ||    |||| |||||   |     |    | | || ||||||||  ||   |||  || ||| |||    || ||||             |||||||| ||||| |  ||||| ||||| ||| | ||||||||||| |||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||
gtaatttaggaaatgcggagccggagctccagaatattttgccggtcgcttgctgcactcattgtgcttagtgccttagtaccacctgttggcaatgttctttacaatgtttgccatgcagGAAGCTGTTGCGATGACTAGATCCATTAAGGACCCAGAAGAGGCTGCAAAGATGCTCTTGCAAGAGGCGTACAAGAGGGAGAGCAGTGACAACATAACTT
















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|86423847|gb|CI062608.1|CI062608
EST:     GTTCCTCATTTCTTGCAAGTGATGGCCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: GTTCCTCA-TTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|8858859|gb|AU096177.1|AU096177
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|27547322|gb|CA765327.2|CA765327
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|66920381|gb|CX107229.1|CX107229
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|88844668|gb|CI021243.1|CI021243
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTTTGGGATGTAGTAACCCATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|38476736|gb|CF960869.1|CF960869
EST:     TCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: TCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|24208771|gb|AU225798.1|AU225798
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|86536657|gb|CI176863.1|CI176863
EST:     AGTTCCTCATTCTGGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|14981649|gb|BI306327.1|BI306327
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|86423540|gb|CI062301.1|CI062301
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCCATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
EST: gi|5003298|gb|AU068447.1|AU068447
EST:     AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAG                         GAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG
genomic: AGTTCCTCATTCTTGCAAGTGATGGGCTGTGGGATGTAGTAACCAATGAGgtaaattcaa ... tcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatcgtattccttgtgcttgatgtagcccccttttgcatttgctcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAGAAGCTCTTGCAAGAGGCCTACAAGAGGGAGAGCAGTGACAACATAACTT
                            cccccttttgcatttg  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattcaagaaaatgaaaagagaagatttttatgtatcttaatcgtattccttgtgcttgatgtagcccccttttgcatttgctcttatgcagGAGGCTGTCGACATGACCAGATCGATTCATGACCCAGAAGAAGCTGCAAAGAAGCTCTTGCAAGAGGCCTACAAGAGGGAGAGCAGTGACAACATAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG