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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagactgttgaaatgatgctgtatattgtatcatctatgtacctttctcaagttttatcggtgttgttatttattctgtttcatatttaattgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAGCTCTTGCTACTTTACCCGGTCCTTTTCACATTACAG

Basic information

species Oryza sativa
transcript LOC_Os02g01720.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G159142_T01 (Zea mays), 3'ss of exon 7
------tagactgttgaa-atgatgctgtatattgtatcatct-atgtacctttctcaagttttatcggtgttgttatttattctgtttcatatttaattgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAGCTCTTGCTACTTTACCCGGTCCTTTTCACATTACAG
      ||    || |||  |||  ||||  |  ||||  | | || |   | ||| |    || |    |||   | |||   | | ||  | ||||        ||||||||||||||||||| |||||||| ||||||||||||||||| |||||||||||||| || || || |||||||||| |||||||
cagagctaattggtagaatgtgaacctgtgaagagtattgtgtcatatcattatctaatacctttttaaggtta--acttaacttctctcccaattaaca------agGCTAAAAGAATGGATGTCGTTGCTGGCGAAACAGCTGGTGTGGAGGGGCAGCTCTTGCTGCTATATCCTGTCCTTTTCATATTACAG
















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|88320028|gb|CI633517.1|CI633517
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGATGTTGTT
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTT
EST: gi|29661903|gb|CB658178.1|CB658178
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
EST: gi|29664288|gb|CB660563.1|CB660563
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
EST: gi|25802938|gb|CA758899.1|CA758899
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
EST: gi|88309328|gb|CI655336.1|CI655336
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGATGTTGTTGCTGGAGAA
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAA
EST: gi|88980837|gb|CI022527.1|CI022527
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
EST: gi|88200565|gb|CI200415.1|CI200415
EST:     GATAGCTCTAGGAAAG                         GCTAAAAGAATGGATTTTGTTGCTGGAGAAACAGCTGTTGTGGAAGGGCAG
genomic: GATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
EST: gi|58687887|gb|CK076574.1|CK076574
EST:     AGAATAGGTACCAGCGTCTAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAG
EST: gi|88310867|gb|CI659470.1|CI659470
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCCTGGTGTGGAAGGGCA
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGC-TGGTGTGGAAGGGCA
EST: gi|58655277|gb|CK043957.1|CK043957
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAACAGAATCGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAG
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAG
EST: gi|88575701|gb|CI669846.1|CI669846
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTG
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTG
EST: gi|88330832|gb|CI636844.1|CI636844
EST:     AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAG                         GCTAAAAGAATGGA
genomic: AGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGA

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), 66 (downstream exon)
Score: 31

ACAACTTTTCCTGCGGTGGGCAATCATGCAAGGAATTGCAATGCATCTACAGAATAGGTACCAGCGTCAAAGATTGCGCACCCGGATAGCTCTAGGAAAGgtaaggttct ... ttgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAGCTCTTGCTACTTTACCCGGTCCTTTTCACATTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcaagttttatcggtgttgttatttattctgtttcatatttaattgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAGCTCTTGCTACTTTACCCGGTCCTTTTCACATTACAG
                                       atttaat  putative branch site (score: 31)
                  ttgttatttattctgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagactgttgaaatgatgctgtatattgtatcatctatgtacctttctcaagttttatcggtgttgttatttattctgtttcatatttaattgcatgcagGCTAAAAGAATGGATGTTGTTGCTGGAGAAACAGCTGGTGTGGAAGGGCAGCTCTTGCTACTTTACCCGGTCCTTTTCACATTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - ctgttga
- - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttca