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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgttcgagccatgctagaaatcctatgcacagatacttggatttgttagatgatatatttggtttttgccctattatatctgctggaagaaagtactcactatgtacactgttgtgataaacatattttatttttcactaaaaaactgcag

Basic information

species Oryza sativa
transcript LOC_Os12g07060.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07060.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G118316_T01 (Zea mays), 5'ss of exon 16
GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgttcgagccatgctagaaatcctatgca-cagatacttggatttgttagatgatatatttggt-ttttgccctattatatctgctggaagaaagtactcactatgtacactgttgtgataaacatattttatttttcactaaaaaactgcag-----------------------
||||| |||||||||||||| ||||| ||||| |||||| ||||||||||| ||||  | |||  |    | ||  | | |  |   ||| ||| |||| |||      |   | |||  ||||||||  | ||| ||| || |||| |  |      |     | | ||    |    ||  |||  ||      | |  | || |                        
GTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAGgtcggttactagagttacaacaaaacccttttttaatggattctttgattagttcagcattcactctggccttttgccccttgataactggtgaaagagaagatattggacagtaaatattagtttttctattcttttgttgaattgatagtattgtaattaacattttatatacttttcag
















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|218480866|gb|FG958004.1|FG958004
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGAGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|218491432|gb|FG970302.1|FG970302
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|33806065|gb|CF328912.1|CF328912
EST:     GGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCTTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|218496597|gb|FG964017.1|FG964017
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|86478861|gb|CI121494.1|CI121494
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|33806063|gb|CF328911.1|CF328911
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|89175720|gb|CI042741.1|CI042741
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88845990|gb|CI084720.1|CI084720
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAGTCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88228631|gb|CI228111.1|CI228111
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|58680289|gb|CK068976.1|CK068976
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|86501480|gb|CI144113.1|CI144113
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88488210|gb|CI425481.1|CI425481
EST:     CAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: CAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88228692|gb|CI228172.1|CI228172
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|58657698|gb|CK046378.1|CK046378
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|218487624|gb|FG950213.1|FG950213
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|86874336|gb|CI335948.1|CI335948
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
EST: gi|88243593|gb|CI243990.1|CI243990
EST:     GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG                         GAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA
genomic: GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCA

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: 49 (upstream exon), 67 (downstream exon)
Score: 23

GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgtt ... aaaactgcagGAATAAAAGCACGGAATTCCCCAGCCTATGGGAATCAGTATATTCACTTCAACGTCCGAGTTCCAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAGgttggttgttcgagccatgctagaaatcctatgcacagatacttggatttgttagatgatatatttggtttttgccctattatatctgctggaagaaagtactcactatgtacactgttgtgataaacatattttatttttcactaaaaaactgcag

- - - - - - - - - - AGGAGA
- - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - -  GCAAAG