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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggataagtttgctttcgaagtattaggtgcaagacaattcagattcgaagtttactcgcattatcctagaagctttgatatgtacagaaattttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCCTCCACCAGCAGCCTAGAGATCCGCTTGATTCAAAGCCAGGATGAAATTC

Basic information

species Oryza sativa
transcript LOC_Os12g40830.3
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G069758_T01 (Zea mays), 3'ss of exon 12
-ggataagtttg---ctttcgaagtattaggtgcaa-gacaattcag-attcgaagtttactcgcattatcctagaagctttgatatgtacagaaattttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCCTCCACCAGCAGCCTAGAGATCCGCTTGATTCAAAGCCAGGATGAAATTC
 || |    |||   |  | | | | | | ||| ||  || ||||    ||   ||||||||   ||  |  ||  | ||     ||| |     | || ||||||||||| || |  ||||||||||||||||||||||  || || || ||||| || ||||||||| |||||||||| ||||| ||||||||||| || || |
ggggtctacttgtggcactagcactgtcatgtgtaataactattcgatgtttacagtttactta-atacttatactaacta----atgcattatgactt-ctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC
















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|88521314|gb|CI448496.1|CI448496
EST:     CCCTTATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGGCTGGGTTTGACCC
genomic: CCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGA-GCTGGGTTTGACCC
EST: gi|427643|gb|D23776.1|D23776
EST:     ACCCTGNTAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGG
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGG
EST: gi|88527260|gb|CI455400.1|CI455400
EST:     ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|88266886|gb|CI368662.1|CI368662
EST:     ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGTCTATAAAAGAGCTGGGTTTGACCCC
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|86885325|gb|CI317085.1|CI317085
EST:     ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|86890174|gb|CI321351.1|CI321351
EST:     ACTGGCGGTATCCAGTTTGCA-                         GCACTCCTAAGGAGAACTGT-GAAGACTATAAAAGAGCTGGCTTTGACCCC
genomic: ACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|13165352|gb|AU174149.1|AU174149
EST:     ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|88540839|gb|CI468912.1|CI468912
EST:     ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|89185094|gb|CI049640.1|CI049640
EST:     ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|88227203|gb|CI228316.1|CI228316
EST:     ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|88473155|gb|CI410426.1|CI410426
EST:     ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|88543303|gb|CI473300.1|CI473300
EST:     ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
genomic: ACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
EST: gi|88546837|gb|CI477088.1|CI477088
EST:     ATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG                         GCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC
genomic: ATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCC

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: 54 (upstream exon), 69 (downstream exon)
Score: 21

AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAGgtatctcagt ... ttttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCCTCCACCAGCAGCCTAGAGATCCGCTTGATTCAAAGCCAGGATGAAATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaagtttactcgcattatcctagaagctttgatatgtacagaaattttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCCTCCACCAGCAGCCTAGAGATCCGCTTGATTCAAAGCCAGGATGAAATTC
                           ctttgat  putative branch site (score: 21)
                                             ttttctgc  putative PPT
                                        agaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggataagtttgctttcgaagtattaggtgcaagacaattcagattcgaagtttactcgcattatcctagaagctttgatatgtacagaaattttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCCTCCACCAGCAGCCTAGAGATCCGCTTGATTCAAAGCCAGGATGAAATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - -tgctttc
- - - - - - - - - - - - - gtgcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atatgta