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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctgcctgccatcactagaaagtagtaatgtgtttttatacggcacaagaaggttatctttgaaagcgctctaaaattgacatgtcaaaccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATCTCTGACGAAGGGGACCGACGGTGATGTAGGGATGGTAAAGGTTGACAAG

Basic information

species Oryza sativa
transcript LOC_Os11g34360.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g34360.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G064366_T01 (Zea mays), 3'ss of exon 4
-----------------------ggctgcctg--ccatcactagaaagtagtaatgtgtttttatacggcacaagaaggttatcttt---------gaaagc-gctctaaaattgacatgtcaaacctt-gtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATCTCTGACGAAGGGGACCGACGGTGATGTAGGGATGGTAAAGGTTGACAAG---
                          ||| |   | |    | ||  || |     ||  ||   ||  |  |||   | || || |            ||| |||||  |||  | ||| |    ||| || |||||| |||||||| || |||||||| ||||| || ||||| |||||||||||||||||||| ||    || ||||| ||||||||||||||  ||||||||   
gtagttatattccattttaaatgcaatgcataatctagtggttgatggttgcttcttgccttaccaccaccaaaggcagctagctgttctatgtgtatgagcagctctgtaatcaatatgccgtttctttgttcagATATGCATATTCTGGTGAAGCTGCTGACGATGACGATGAGGAATCTCAATCTCTGACGAAAGGA---GATGGTGAAGTAGGGATGGTAAAAATTGACAAGGAC
















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|86430492|gb|CI082915.1|CI082915
EST:     TTGCTTCTTGTGATTTGTAATCTATGGGCGCCATCCCAGAGCTCACAAAG                         ATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTATGGGCGCCATCCCAGAGCTCACAAAGgttaaatctt ... ccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
EST: gi|89161780|gb|CI100940.1|CI100940
EST:     TTGCTTCTTGTGATTTGTNATCTATGGGCGCCATCCCAGAGCTCACAAAG                         ATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCCAAT
genomic: TTGCTTCTTGTGATTTGTTATCTATGGGCGCCATCCCAGAGCTCACAAAGgttaaatctt ... ccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCT-CAAT
EST: gi|86859957|gb|CI321935.1|CI321935
EST:     CCATCCCAGAGCTCACAAAG                         ATACGCATATTCAGGC-AAGCTGCCGACGACGATGATGAAGAATCTCAATC
genomic: CCATCCCAGAGCTCACAAAGgttaaatctt ... ccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
EST: gi|89163870|gb|CI100760.1|CI100760
EST:     TGGGCGCCATCCCAGAGCTCACAAAG                         ATACGCATATTCAGGCGAAGCGGCCGACGACGATGATGAAGAATCTCAATC
genomic: TGGGCGCCATCCCAGAGCTCACAAAGgttaaatctt ... ccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
EST: gi|88964712|gb|CI070058.1|CI070058
EST:     TTGCTTCTTGTGATTTGTNATCTATGGGCGCCATCCCAGAGCTCACAAAG                         ATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTATGGGCGCCATCCCAGAGCTCACAAAGgttaaatctt ... ccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
EST: gi|88989080|gb|CI042193.1|CI042193
EST:     TTGCTTCTTGTGATTTGTNATCTATGGGCGCCATCCCAGAGCTCACAAAG                         ATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTATGGGCGCCATCCCAGAGCTCACAAAGgttaaatctt ... ccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
EST: gi|87012860|gb|CI297087.1|CI297087
EST:     TTGCTTCTTGTGATTTGTTATCTATGGGCGCCATCCCAGAGCTCACAAAG                         ATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTATGGGCGCCATCCCAGAGCTCACAAAGgttaaatctt ... ccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
EST: gi|86417691|gb|CI031900.1|CI031900
EST:     TTGCTTCTTGTGATTTGTTATCTATGGGCGCCATCCCAGAGCTCACAAAG                         ATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC
genomic: TTGCTTCTTGTGATTTGTTATCTATGGGCGCCATCCCAGAGCTCACAAAGgttaaatctt ... ccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATC

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), 72 (downstream exon)
Score: 21

GGCAGAGCGCATGGATCATAACTGCATTCTGGGACGTTCTTGCATTTGTTTTGCTTCTTGTGATTTGTTATCTATGGGCGCCATCCCAGAGCTCACAAAGgttaaatctt ... ccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATCTCTGACGAAGGGGACCGACGGTGATGTAGGGATGGTAAAGGTTGACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaagaaggttatctttgaaagcgctctaaaattgacatgtcaaaccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATCTCTGACGAAGGGGACCGACGGTGATGTAGGGATGGTAAAGGTTGACAAG
                              aattgac  putative branch site (score: 21)
                                             ccttgtcc  putative PPT
                         tctaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctgcctgccatcactagaaagtagtaatgtgtttttatacggcacaagaaggttatctttgaaagcgctctaaaattgacatgtcaaaccttgtccagATACGCATATTCAGGCGAAGCTGCCGACGACGATGATGAAGAATCTCAATCTCTGACGAAGGGGACCGACGGTGATGTAGGGATGGTAAAGGTTGACAAG

- -tgcctgc
- - - - - - - - - - - - - - -tgtgttt
- - - - - - - - - - - - - - - - - - - - - -gcacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatg