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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaaaaaaaaaaagacttatctaccatttcaacatttttttttgtggtgtactttgtttctcattgatatactgaccaacatacatcatcattaattgcattttatattctattatgatgcatgtttatcaacactacttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGGATATTGGTGCAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g07760.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G128114_T01 (Zea mays), 3'ss of exon 11
gtaagcaaaaaaaaaaaagacttatctaccatttcaacatttttttttgtggtgtactttgtttctcattgatatactgaccaacatacatcatcattaattgcattttatattctattatgatgcatgtttatcaacactacttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGGATATTGGTGCAAGAAG
                                       |  || | | |    ||||||||||  | ||| | |        |  ||   |||    |        || |||| || ||| ||  || || | |||  | |  | ||| ||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||
---------------------------------------tcattatgtatataatactttgtttggctttgttgt------tgaagtattgcattgcca--------ttgtattttaatataatcaatattcaccaagtccatatgtgtgcagCTTGCTGCCAAGTTCCGTAACAGTGGACAGACATGTGTTTGTGCAAACAGGATATTGGTGCAAGAAG

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G119482_T01 (Zea mays), 3'ss of exon 11
gtaagcaaaaaaaaaaaagacttatctaccatttcaacatttttttttgtggtgtactttgtttctcattgatatactgaccaacatacatcatcattaattgcattttatattctattatgatgcatgtttatcaacactacttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGGATATTGGTGCAAGAAG
                                   |  |  ||  |||| | |  |||| ||      ||||  |  |||  || ||         |  |||||   ||  ||| || | ||||  ||||| || ||  | |  | ||| ||||||||||| ||||| |||||||| |||||||||||||| ||||||||||||||||||||||||||||
-----------------------------------atgaggttcatttgagatagacttcgt------ttgacttgttga--aatat---------tgcattgc-ccttgcattttaatgtgatcaatgttcatgaaatccatatgtgtgcagCTTGCTGCCAAGTTTCGTAACAGTGGACAGACATGTGTTTGTGCAAACAGGATATTGGTGCAAGAAG

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G17450.1 (Glycine max), 3'ss of exon 11
gtaagcaaaaaaaaaaaagacttatctaccatttcaacatttttttttgtggtgtactttgtttctcattgatatactgaccaacatacatcatcattaattgcattttatattctattatgatgcatgtttatcaacactacttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGGATATTGGTGCAAGAAG
                                             |   || |  | |       | |  ||  | |||     |   | ||  |  |  ||  ||  |||  |  || || ||     ||||| ||    | | |     ||||||| || |||||||||||||| ||||| |||||||| |||||||| || ||  | ||||||||||
---------------------------------------------taattgctaaaatggaaagttaagggacgtgctgtgattctcccttcccctctgttttgatcatatcattaatcataatat---tttattaatttgattgc-----agCTTGCAGCAAAGTTCCGTAACAGTGGACAAACATGTGTTTGTGCAAATAGAATTATTGTGCAAGAAG

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 11
gtaagcaaaaaaaaaaaagacttatctaccatttcaacatttttttttgtggtgtactttgtttctcattgatatactgaccaacatacatcatcattaattgcattttatattctattatgatgcatgtttatcaacactacttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGGATATTGGTGCAAGAAG
                                             |   || |  | ||      | |  | | | |||     |   | ||  |  |  |   ||  |||  |  || || |      || || ||      ||   | |||||||| || |||||||||||||| ||||| |||||||| |||||||| || ||  | ||||||||||
---------------------------------------------taattgctaaaattgaaagttaaggggtgtgctgtgattctcccttcccctctgttatgatgatatcattaatcataacat---ttcattaat-----ttggttgcagCTTGCAGCAAAGTTCCGTAACAGTGGACAAACATGTGTTTGTGCAAATAGAATTATTGTGCAAGAAG

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv19s0085g00880.t01 (Vitis vinifera), 3'ss of exon 11
gtaagcaaaaaaaaaaaagacttatctaccatttcaacatttttttttgtggtgtactttgtttctcattgatatactgaccaacatacat-catcattaattgcattttatattctattatgatgcatgtttatcaacactacttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGGATATTGGTGCAAGAAG
                                                || ||| |  | |  | |  ||  |  | |   ||||||   | |||  | | ||    | | |   | ||| |    |     | |  |  || ||| ||  ||||||| | | |||||||||||||| ||||| |||||||| |||||||| || ||| | ||||| ||||
-----------------------------------------------agtagtgaaaatggacttt-gttatttaatttgacaacatttctgcattctcagtt----tctgtgcaccattgtttaactaaaatgtggaatcttcttttg--cagCTTGGTACAAAGTTCCGTAACAGTGGACAAACATGTGTTTGTGCAAATAGAATACTTGTGCAGGAAG

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|163925517|gb|EG715386.1|EG715386
EST:     CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT                         CTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
genomic: CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGTgtaagcaaaa ... ttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
EST: gi|218498176|gb|FG949780.1|FG949780
EST:     CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT                         CTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
genomic: CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGTgtaagcaaaa ... ttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
EST: gi|218482143|gb|FG968613.1|FG968613
EST:     CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT                         CTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
genomic: CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGTgtaagcaaaa ... ttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
EST: gi|218492318|gb|FG946726.1|FG946726
EST:     CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT                         CTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
genomic: CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGTgtaagcaaaa ... ttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
EST: gi|218490731|gb|FG966180.1|FG966180
EST:     CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT                         CTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
genomic: CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGTgtaagcaaaa ... ttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
EST: gi|66918914|gb|CX105762.1|CX105762
EST:     CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT                         CTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
genomic: CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGTgtaagcaaaa ... ttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
EST: gi|58694576|gb|CK083263.1|CK083263
EST:     CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT                         CTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG
genomic: CTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGTgtaagcaaaa ... ttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgcattttatattctattatgatgcatgtttatcaacactacttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGGATATTGGTGCAAGAAG
 cattaat  putative branch site (score: 3)
                                            cttctgttc  putative PPT
      attttatattctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaaaaaaaaaaagacttatctaccatttcaacatttttttttgtggtgtactttgtttctcattgatatactgaccaacatacatcatcattaattgcattttatattctattatgatgcatgtttatcaacactacttctgttcagCTTGCTGCTAAGTTCCGTAACAGCGGACAGACATGTGTATGTGCAAACAGGATATTGGTGCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG