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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatagtgacagacatgggaaaagtttctgctgagttattcaacatatttgtctacaattcttttgtatgtaatttgacatgagtccaatttgcctgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTTCAGGATGATGCTGCAAAAGAGGGAGTCGTGCTG

Basic information

species Oryza sativa
transcript LOC_Os12g01140.5
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 8
gtactatagtgacagacatgggaaaagtttctgctgagttattcaacatatttgtctacaattcttttgtatgtaatttgacatgagtccaatttgcctgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTTCAGGATGATGCTGCAAAAGAGGGAGTCGTGCTG
||||| || | | ||| ||| ||    ||| |       ||   |  || || || |  || | |||  ||||  |||| | |||  |||| ||||   || ||| ||||||||||||| ||||| |||||||||||||||||||||||||||| |||||  || | |||||||||||| || | | | |||
gtactgtaataagagatatgaga----ttttt-------tacgtagtat-ttggtttggaactatttcatatg--atttaagatgcatccattttgatggttgattagGGTGATGTTCAATACTTCATTGGGGTTCAATTGGATGGAACTGAGCGTGTTCGAGAGGCTGCTGCAAAAGATGGTGCCATACTG
















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|29624477|gb|CB629488.1|CB629488
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29630119|gb|CB635128.1|CB635128
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGCT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29681859|gb|CB678134.1|CB678134
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29624448|gb|CB629459.1|CB629459
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29641853|gb|CB646860.1|CB646860
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|2317379|gb|C22433.1|C22433
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTTGGATGGGACTGAGCATGT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATT-GGATGGAACTGAGCATGT
EST: gi|29672018|gb|CB668293.1|CB668293
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29628293|gb|CB633304.1|CB633304
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29613611|gb|CB618624.1|CB618624
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGCT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29678744|gb|CB675019.1|CB675019
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29627346|gb|CB632357.1|CB632357
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGCT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29630466|gb|CB635475.1|CB635475
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGCT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|2317377|gb|C22431.1|C22431
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGGTTCAATTGGATGGGACTGAGCATGT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGG-TTCAATTGGATGGAACTGAGCATGT
EST: gi|29624450|gb|CB629461.1|CB629461
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
EST: gi|29646710|gb|CB651717.1|CB651717
EST:     GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG                         GGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT
genomic: GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAGgtactatagt ... tgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctacaattcttttgtatgtaatttgacatgagtccaatttgcctgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTTCAGGATGATGCTGCAAAAGAGGGAGTCGTGCTG
                      atttgac  putative branch site (score: 4)
                                       tttgcct  putative PPT
           ttttgtatgtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactatagtgacagacatgggaaaagtttctgctgagttattcaacatatttgtctacaattcttttgtatgtaatttgacatgagtccaatttgcctgtggatcagGGTGATGTTCAGTACTTTATTGGGGTTCAATTGGATGGAACTGAGCATGTTCAGGATGATGCTGCAAAAGAGGGAGTCGTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG