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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtgttcatcacaaatttacaatattcttatttgataatcacattgtcttatctgtttgttttctttatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCGAAAGGAGACGATCATGTGCCCTTCAGGAACTCAAAACTTACATACCTTT

Basic information

species Oryza sativa
transcript LOC_Os04g53760.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 14
gtgagtgt--gttcatcacaaatttacaatattcttatttgataatcacattgtcttatctgtttgttttctttatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCGAAAGGAGACGATCATGTGCCCTTCAGGAACTCAAAACTTACATACCTTT
||| ||||  | | | || | |||| ||||||||  |       || |  || | |  ||   ||  ||  || ||| | ||| ||||||||||||||||||| ||| | |||||||| ||||| || || || |||||||| || || || || ||||| || ||||||||||||||||| |
gtgggtgtttgcttaccatagatttccaatattccaagcattctataatgttatat--tcaaattactt--ttaatgctccagTCAATCAATAAAAGCTTGTCGGCTTTGAGCGATGTAATCTTCGCGATCGCAAAAGGAGATGACCACGTTCCGTTCAGAAATTCAAAACTTACATACCTAT

upper sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA12G16580.1 (Glycine max), 3'ss of exon 15
gtgagtgtgttcatcacaaatttacaat-----attcttatttgataatcacattgtcttatctgtttgttttctttatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCGAAAGGAGACGATCATGTGCCCTTCAGGAACTCAAAACTTACATACCTTT
||  |     || |      ||||   |      | ||||||||||  |||||| || | | || | | |  ||| ||     ||||||||||| ||||| || ||| | || || |||||||| || ||  | || ||    || ||||||||||| |||||||||||||| |||||||| ||  
gtatgcaaagtcgtggtgcttttattctcacttgtgcttatttgatt-tcacatagtttaaactctctttcatctgtaa---ccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCCAAGAAGGAGGATCATGTGCCATTCAGGAACTCAAAGCTTACATATCTCC
















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|86855868|gb|CI271087.1|CI271087
EST:     AACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAG                         GCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
genomic: AACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
EST: gi|29637660|gb|CB642669.1|CB642669
EST:     AACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAG                         GCAATCAATAAAAGCTTGTCAGCTCTTAGCGAGGTTATCTTTGCAATTGCG
genomic: AACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
EST: gi|89184723|gb|CI007148.1|CI007148
EST:     GGTGATCGTTTGAAGGAAACTCAG                         GCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
genomic: GGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
EST: gi|86482430|gb|CI125063.1|CI125063
EST:     CCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAG                         GCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
genomic: CCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
EST: gi|88985287|gb|CI006941.1|CI006941
EST:     AACGCCTTGCTAAAAGTGGCTCCCCGGGTGATCGTTTGAAGGAAACTCAG                         GCCATCCATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
genomic: AACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
EST: gi|87022822|gb|CI269758.1|CI269758
EST:     AACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAG                         GCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAGTTGCG
genomic: AACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
EST: gi|88980972|gb|CI021099.1|CI021099
EST:     GGTGATCGTTTGAAGGAAACTCAG                         GCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
genomic: GGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
EST: gi|427624|gb|D23757.1|D23757
EST:     GTGATCGTTTGAAGGAAACTCAG                         GCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
genomic: GTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
EST: gi|87021429|gb|CI274036.1|CI274036
EST:     AACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAG                         GCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
genomic: AACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG
EST: gi|58657773|gb|CK046453.1|CK046453
EST:     CACGGGTGATCGTTTGAAGGAAACTCAG                         GCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCGATTGCG
genomic: CACGGGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCG

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: 66 (upstream exon), 64 (downstream exon)
Score: 6

TGGGCAACAAGTCCAAGGTGTCCTTAACTTGATTGATTTAGCTGGCAGTGAACGCCTTGCTAAAAGTGGCTCCACGGGTGATCGTTTGAAGGAAACTCAGgtgagtgtgt ... tatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCGAAAGGAGACGATCATGTGCCCTTCAGGAACTCAAAACTTACATACCTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattcttatttgataatcacattgtcttatctgtttgttttctttatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCGAAAGGAGACGATCATGTGCCCTTCAGGAACTCAAAACTTACATACCTTT
        atttgat  putative branch site (score: 6)
                         tcttatctgtttgttt  putative PPT
      ttatttgataatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtgttcatcacaaatttacaatattcttatttgataatcacattgtcttatctgtttgttttctttatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCGAAAGGAGACGATCATGTGCCCTTCAGGAACTCAAAACTTACATACCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA