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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctaacttaatcttcatcaaagtatttccttgtgaggattatgtaatactccctccagttttttttatatgacgttggctagttcaaatttgaactagtcagcgttatacatataaagatggaggcagtactaccttttataaactaataattttggacttgtgattcactagaatgctttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGTAAGCAAGCCTATCGCATGGCTTGCCCCCGACTTCTAAAGTTGCAGACGT

Basic information

species Oryza sativa
transcript LOC_Os01g53700.1
intron # 12
splice site 3'
intron type U2

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|88264876|gb|CI367527.1|CI367527
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88906152|gb|CI375224.1|CI375224
EST:     CCAAGAAGATCATTTCATCACCCCTTACACTGGGCATCATGGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAG
genomic: CCAAGAAGATCATTTCATCACCCCTTACACT-GGCATCAT-GGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAG
EST: gi|89191950|gb|CI250891.1|CI250891
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88838739|gb|CI376277.1|CI376277
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88964180|gb|CI045373.1|CI045373
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|89166280|gb|CI103370.1|CI103370
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88834759|gb|CI370062.1|CI370062
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88250927|gb|CI248778.1|CI248778
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|5701695|gb|AU063482.2|AU063482
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|86893269|gb|CI313403.1|CI313403
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88267554|gb|CI379489.1|CI379489
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|86593940|gb|CI260169.1|CI260169
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88268173|gb|CI377910.1|CI377910
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGTGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88843303|gb|CI372203.1|CI372203
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|9864980|gb|AU100730.1|AU100730
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|86841142|gb|CI342900.1|CI342900
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88297257|gb|CI545347.1|CI545347
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|86434084|gb|CI094427.1|CI094427
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|87021256|gb|CI295315.1|CI295315
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAG
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAG
EST: gi|88436304|gb|CI519223.1|CI519223
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|88967984|gb|CI098226.1|CI098226
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|58597827|gb|CK008355.1|CK008355
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGT
EST: gi|163920798|gb|EG710061.1|EG710061
EST:     TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACG                         TTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTTCTCAAAG
genomic: TGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTT-CTCAAAG

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: 70 (upstream exon), 44 (downstream exon)
Score: 22

CATTTCTTGAAAGATCTTGAAGCAATCACCTTGAATGACATTTCTTCTACTGCCAAGAAGATCATTTCATCACCCCTTACACTGGCATCATGGGGTGACGgtatgttcta ... tttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGTAAGCAAGCCTATCGCATGGCTTGCCCCCGACTTCTAAAGTTGCAGACGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttataaactaataattttggacttgtgattcactagaatgctttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGTAAGCAAGCCTATCGCATGGCTTGCCCCCGACTTCTAAAGTTGCAGACGT
         aactaat  putative branch site (score: 22)
                                          tgctttctt  putative PPT
     tataaactaataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttctaacttaatcttcatcaaagtatttccttgtgaggattatgtaatactccctccagttttttttatatgacgttggctagttcaaatttgaactagtcagcgttatacatataaagatggaggcagtactaccttttataaactaataattttggacttgtgattcactagaatgctttcttgcagTTATTCATGTCCCGAGCTATGAATCTGTTAGCCAGAAGTTTTTCTCAAAGTAAGCAAGCCTATCGCATGGCTTGCCCCCGACTTCTAAAGTTGCAGACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG