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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatgatgcattttcactgataagcttctctcttgatgatgcttttaggtttgcatttagacgattttatgcaagagcggttttgtaccacaaaa...

Basic information

species Oryza sativa
transcript LOC_Os08g41950.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41950.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G159397_T01 (Zea mays), 5'ss of exon 3
CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatgatgcattttcactgataagcttctctcttgatgatgcttttaggtttgcatttagacgattttatgcaagagcggttttgtaccacaaaa--
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CAACTGAAAAGTAGCCGCAATGAGTACCTCAAACTGAAGGCACGTGTTGATAATTTACAGCGGACTCAAAGgtgagttctgttatacaattaa-gataaatttgttatttctgtacatacttaaaaatagcaatttatgtttgaatgtgctt-tgttttgggaaaacatgctt
















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|88401388|gb|CI585944.1|CI585944
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAACATCTTGATTCATTA
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCATTA
EST: gi|58663584|gb|CK052270.1|CK052270
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
EST: gi|88720377|gb|CI743676.1|CI743676
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAAGATCTTGATTCAT
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCAT
EST: gi|2799584|gb|AA752573.1|AA752573
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
EST: gi|40491399|gb|BX901494.1|BX901494
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
EST: gi|163926627|gb|EG713643.1|EG713643
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
EST: gi|24208827|gb|AU225854.1|AU225854
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
EST: gi|88461647|gb|CI695489.1|CI695489
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAAGATCTTGATTCA
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCA
EST: gi|88726869|gb|CI750524.1|CI750524
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
EST: gi|66932169|gb|CX119017.1|CX119017
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAG
EST: gi|88313445|gb|CI671563.1|CI671563
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG                         AAATTTGCTGGGTG
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTG
EST: gi|88581413|gb|CI698397.1|CI698397
EST:     GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCCAAG                         AAATTTGCTGGG
genomic: GAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 174

CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatg ... actatgacagAAATTTGCTGGGTGAAGATCTTGATTCATTAGGCATAAAAGAGCTCGAGAGCCTAGAGAAGCAGCTTGATTCATCCCTGAAGCACGTCAGAACTACAAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAGgcaagttatgatgcattttcactgataagcttctctcttgatgatgcttttaggtttgcatttagacgattttatgcaagagcggttttgtaccacaaaa

- - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctctc