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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtatcttgctgtcccattgtcccagcatgtaacaaaatggtgttttcattccttatttattagaagttacatgagctgactaagtcccgattgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCCTATATATTACTATGTGTTCAATTCTCTCCTATTTTCACTACTTGTTCTT

Basic information

species Oryza sativa
transcript LOC_Os02g37080.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g37080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G170868_T01 (Zea mays), 3'ss of exon 4
agtatcttgctgtcccattgtc-ccagcatgtaacaaaatggtgttttcattccttatttattagaagttacatgagctgactaagtcccgattgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCCTATATATTACTATGTGTTCAATTCTCTCCTATTTTCACTACTTGTTCTT
|  | |   |   |||| | || |||    |    | |||    |  |      ||  |   |     | |||||| |||||| |  |||  |||  |||||||||| ||||||||||| |||||||| ||||||||||||||||||||||||||||| || |||||||||||||| || |||||||||||||||||||| 
acaaacaaacaaacccagtttcaccacttcgctttagaataaactaattgaatgtttctggattcttttcacatgatctgactgaa-cccatttgtctcagCTATGAGGTCTTGTTGACTTTGGACAAAAAGAAGCACAATTTTGATGGTCCTATATACTATTATGTGTTCAATTCCCTTCTATTTTCACTACTTGTTCTC

upper sequence: LOC_Os02g37080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G444643_T01 (Zea mays), 3'ss of exon 5
---agtatcttgctgtcccattgtcccagcatgtaacaaaatggtgttttcattccttatttattagaagttacatgagctgactaagtcccgattgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCCTATATATTACTATGTGTTCAATTCTCTCCTATTTTCACTACTTGTTCTT
   |  |     | |   ||    |   || ||||  ||          ||| |  || |  |||     || ||||| |||||||| |||   | | ||||||||||| ||||||||||| |||||||| ||||||||||| ||||||||||||||||| || |||||||||||||| || |||||||||||||||||||| 
aaaaaaagaaaacagattcacca-ctttgcttgtag-aagtaaaccaactcaatgtttttggattctttttttcatgatctgactaaatcc-attcgtttcagCTATGAGGTCTTGTTGACTTTGGACAAAAAGAAGCACAACTTTGATGGTCCTATATACTATTATGTGTTCAATTCCCTTCTATTTTCACTACTTGTTCTC
















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|29671597|gb|CB667872.1|CB667872
EST:     GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAG                         CTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
genomic: GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAGgtaaatgtga ... attgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
EST: gi|88723508|gb|CI747018.1|CI747018
EST:     GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAG                         CTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
genomic: GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAGgtaaatgtga ... attgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
EST: gi|29664916|gb|CB661191.1|CB661191
EST:     GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAG                         CTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
genomic: GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAGgtaaatgtga ... attgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
EST: gi|29659632|gb|CB655907.1|CB655907
EST:     GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAG                         CTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
genomic: GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAGgtaaatgtga ... attgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
EST: gi|29658422|gb|CB654697.1|CB654697
EST:     GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAG                         CTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
genomic: GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAGgtaaatgtga ... attgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
EST: gi|29685057|gb|CB681332.1|CB681332
EST:     GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAG                         CTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
genomic: GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAGgtaaatgtga ... attgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
EST: gi|33683971|gb|CF312210.1|CF312210
EST:     GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAG                         CTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC
genomic: GTTCTTCTCCGTCTCACATATTTTCCGTTCTGGATTCTCAGAAGTACAAGgtaaatgtga ... attgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattccttatttattagaagttacatgagctgactaagtcccgattgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCCTATATATTACTATGTGTTCAATTCTCTCCTATTTTCACTACTTGTTCTT
                             agctgac  putative branch site (score: 3)
                                              ttgcttc  putative PPT
        ttatttattagaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtatcttgctgtcccattgtcccagcatgtaacaaaatggtgttttcattccttatttattagaagttacatgagctgactaagtcccgattgcttcagCTATGAAGTCTTGTTGACCTTGGACAAGAAGAAGCACAATTTTGATGGTCCTATATATTACTATGTGTTCAATTCTCTCCTATTTTCACTACTTGTTCTT

- - - -tgctgtc
- - - - - - - - - - - - -gcatgta
- - - - - - - - - - - - - - - - acaaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgagc