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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgtcatcttgtcttctactggttgatttcttgtttcttctcctgtggatgaaccgcgggatcccatcttacaattgattccttttcttttcttgactgtatatgttcttgattttggggatttttggtgggtttttattattagtattgttgttaatctgtggagatggattcgtacgattcgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGACATACCAGCTGCAGGTCGACTTCCCTGAGCATTATCCCATGGAGGCGCCT

Basic information

species Oryza sativa
transcript LOC_Os12g44000.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 2
gtcgtcatcttgtcttctactggttgatttcttgtttcttctcctgtggatgaaccgcgggatcccatcttacaattgattccttttcttttcttgactgtatatgttcttgattttggggatttttggtgggtttttattattagtattgttgttaatctgtggagatggattcgtacgattcgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGACATACCAGCTGCAGGTCGACTTCCCTGAGCATTATCCCATGGAGGCGCCT
                                                                   ||||   ||  | | |||||||||    ||    | |||||||      || |||     ||||| |||  | ||   |       | | ||      ||||   |  ||     |  |  |  ||||||||||| |||||||| |||||||||||||| || |||||||||||||| |||||| ||||||| |||||||||||||||||||| |||||||| |||
-------------------------------------------------------------------tcttgatatctagtgcttttcttt----gatctcacatgttctc-----tgtgga-----ggtggatttggactacctg-------gctgat-----aagataattatgtctcgataactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCT

upper sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 2
gtcgtcatcttgtcttctactggttgatttcttgtttcttctcctgtggatgaaccgcgggatcccatcttacaattgattccttttcttttcttgactgtatatgttctt-gattttggggatttttggtgggtttttattattagtattgttgttaatctgtggagatggattcgtacgattcgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGACATACCAGCTGCAGGTCGACTTCCCTGAGCATTATCCCATGGAGGCGCCT
                                                                                        | ||  |  ||     | ||||| ||| |  |   || |  ||||   |  |||  | |      |      |||    |||   |   |  |  |  |  || ||||||||||| ||||||||||||||||||||||| || |||||||||||| | |||||| ||||||| |||||||||||||||||||| |||||||| |||
----------------------------------------------------------------------------------------tcttgatatctagggcttttctttgatctcagtcgttctctgtggaggtggatt--tgg----actacctgcctgataggataattctctctggataactgaacagGTGGGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCT
















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|163920049|gb|EG709843.1|EG709843
EST:     GTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCCAAAG                         GTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGAC
genomic: GTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCCAAAGgtcgtcatct ... cgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGAC
EST: gi|8857593|gb|AU094911.1|AU094911
EST:     GTCAGCCCT-CCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCCAAAG                         GTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGAC
genomic: GTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCCAAAGgtcgtcatct ... cgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGAC
EST: gi|58593809|gb|CF992117.1|CF992117
EST:     GTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCCAAAG                         GTGGGTAATCGAGGTCACCGGAGCGGGGGGCACGCTCTACGCCGGCGAGAC
genomic: GTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCCAAAGgtcgtcatct ... cgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGAC
EST: gi|8857008|gb|AU094326.1|AU094326
EST:     TCAGCCCTCCTTCCGGGTNCAAG-ACAGGGTCTCCGAT-ACCNTCCAAAG                         GTGGGTAATCGAGGTCACCGGAGCGNCGGGCACGCTCTACGCCGGCGAGA
genomic: TCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACC-TCCAAAGgtcgtcatct ... cgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGA
EST: gi|5851049|gb|AU078221.1|AU078221
EST:     GTCAGCCCT-CCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCCAAAG                         GTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGAC
genomic: GTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCCAAAGgtcgtcatct ... cgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGAC
EST: gi|8856902|gb|AU094220.1|AU094220
EST:     CGGGTTCCAAGTACAGGGTCTCCGATAACCTCCAAAG                         GTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTNTACGCCGGCGAGAC
genomic: CGGGTT-CAAGTACAGGGTCTCCGATAACCTCCAAAGgtcgtcatct ... cgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattagtattgttgttaatctgtggagatggattcgtacgattcgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGACATACCAGCTGCAGGTCGACTTCCCTGAGCATTATCCCATGGAGGCGCCT
              tgttaat  putative branch site (score: 3)
                                           ttcgcct  putative PPT
             ttgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcgtcatcttgtcttctactggttgatttcttgtttcttctcctgtggatgaaccgcgggatcccatcttacaattgattccttttcttttcttgactgtatatgttcttgattttggggatttttggtgggtttttattattagtattgttgttaatctgtggagatggattcgtacgattcgcctaatagGTGGGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGACATACCAGCTGCAGGTCGACTTCCCTGAGCATTATCCCATGGAGGCGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG