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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccttctatgctgttgttccttttatatttggttccataattagtctttccaaattcatattctcactactctgtaatttgttgctttctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCTTGATCAATATTCTGATCTGGGGTGTTGTTGGAACCTTCTGGTGGAAACT

Basic information

species Oryza sativa
transcript LOC_Os09g29430.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29430.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G040933_T02 (Zea mays), 3'ss of exon 4
------tttccttctatgctgttgttccttttatatttggt-tccataattagtctttccaaattcatattctcactactctgtaatttgttgctttctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCTTGATCAATATTCTGATCTGGGGTGTTGTTGGAACCTTCTGGTGGAAACT
       ||  ||  | || |     |  |   | ||| || |  | |  ||  |  |  |||||  ||| |  | ||       |  |||| ||||   | |||||| |||||| | |||||||||||||| |||||| |||||||  |||||||||||   || |   | |||||||| |||||||||||| ||||||||||| |
ggatatctttttttaaagcgggcaagcggtccttcttttgtatatagagataaccccttgaaattggtatgcagatta-------acctgttacttttgttgtgcagCCGGGTATATGGAGCTTCCAGATGTTTTCAGGCTGGGTTTTATAACAGCCTTGGCTAACACGTTAATCTGGGGAGTTGTTGGAACCATCTGGTGGAAATT
















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|88537497|gb|CI464448.1|CI464448
EST:     TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTTTACTTTGGAG                         CGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
genomic: TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
EST: gi|88975494|gb|CI021576.1|CI021576
EST:     TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAG                         CGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
genomic: TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
EST: gi|25803590|gb|CA759551.1|CA759551
EST:     TGGTGCACTAACCCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAG                         CGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
genomic: TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
EST: gi|88530445|gb|CI458840.1|CI458840
EST:     TGGTGCACTAACTCATTATAGTAGCGGACAGGCTCCAGTGTACTTTGGAG                         CGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
genomic: TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
EST: gi|88243141|gb|CI244263.1|CI244263
EST:     TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAG                         CGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
genomic: TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
EST: gi|29617553|gb|CB622565.1|CB622565
EST:     TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAG                         CGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
genomic: TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
EST: gi|12623185|gb|AU173398.1|AU173398
EST:     TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAG                         CGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
genomic: TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
EST: gi|89164602|gb|CI101690.1|CI101690
EST:     TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAG                         CGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
genomic: TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
EST: gi|88526141|gb|CI453191.1|CI453191
EST:     TGGTGCACTAACTCATTATAGTANCGGACAGGCTGCAGTGTACTTTGGAG                         CGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT
genomic: TGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCT

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: 73 (upstream exon), 40 (downstream exon)
Score: 12

GTTCCTCGAGTGCTGTCAGCTCTTGCTTTGGCATTCAACACAAATCTGTTTGGTGCACTAACTCATTATAGTAGCGGACAGGCTGCAGTGTACTTTGGAGgtaaattcat ... ctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCTTGATCAATATTCTGATCTGGGGTGTTGTTGGAACCTTCTGGTGGAAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctttccaaattcatattctcactactctgtaatttgttgctttctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCTTGATCAATATTCTGATCTGGGGTGTTGTTGGAACCTTCTGGTGGAAACT
                 ttctcac  putative branch site (score: 12)
                                         ctttctatct  putative PPT
        aaattcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccttctatgctgttgttccttttatatttggttccataattagtctttccaaattcatattctcactactctgtaatttgttgctttctatctgcagCGGGGTATCTTGAGCTTCCAGATGTATTCAGGATGGGTTTCGTAACAGCCTTGATCAATATTCTGATCTGGGGTGTTGTTGGAACCTTCTGGTGGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct