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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtgaatgaaatattttcttaagtgcccatgttgcagttgctactatttttcctaactatgtatattccctcgaccatctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATTGATGCTGTTGACCGTGATACAGTAATGGAAACAGCTAAGGATTTCATAA

Basic information

species Oryza sativa
transcript LOC_Os01g51390.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51390.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G827505_T01 (Zea mays), 3'ss of exon 7
gtatggtgaatgaaatattttcttaagtgcccatgttgcagttgctactatttttcctaactatgtatattccct-cgaccatctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATTGATGCTGTTGACCGTGATACAGTAATGGAAACAGCTAAGGATTTCATAA
||||  |     ||     |||| |      |  |  |||| | || | ||  |   |||  |  | | ||  |  | || ||||    ||||||||||| ||||||||||| ||||| ||| ||||||||||||| |||||||||||||||||| ||| ||||||||||||||| || ||||| | |||||
gtattctagcctaagc---ttctcaga----ctagcagcagcttctcccatcctgattaataagattttttttccgcaactatctcatgcagATGCTAACTTATGGGCGAGTCATGCCGTTCCTAGAGCTTTTTGCACGCATTGATGCTGTTGACTGTGCTACAGTAATGGAAACTGCCAAGGAGTACATAA
















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|86598949|gb|CI355566.1|CI355566
EST:     CTGTTTCTGAAAATAACGGCCGTCAG                         ATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: CTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|86863825|gb|CI332840.1|CI332840
EST:     TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAG                         ATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|88455497|gb|CI521717.1|CI521717
EST:     GTTTCTGAAAATAACGGCCGTCAG                         ATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: GTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|86893110|gb|CI333407.1|CI333407
EST:     CTGAAAATAACGGCCGTCAG                         ATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: CTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|86899803|gb|CI327590.1|CI327590
EST:     TTGACGGATCCACTGCTGTTTCTTAAAATAACGGCCGTCAG                         ACGCTAACGTAT-GGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: TTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|8527222|gb|AU092037.1|AU092037
EST:     TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAG                         ATGCTAACGTNTGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|86603125|gb|CI357489.1|CI357489
EST:     TACTTCACATTGACGAATCCACTGCTGTTTCTGAAAATAACGGCCGTCAG                         ATGCTAACGTATGTGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|33687242|gb|CF315481.1|CF315481
EST:     TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAG                         ATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|86865382|gb|CI330888.1|CI330888
EST:     TTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAG                         ATGCTAACGTATGGGCGAGTAATCCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: TTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|117220685|gb|CT852401.1|CT852401
EST:     TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAG                         ATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|86870480|gb|CI320576.1|CI320576
EST:     TACTTCACATTGACGGATCCACTCCTGTTTCTGAAAATAACGCCCGTCAG                         ATGCTAACGTATGGGCGA-TAATCCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
EST: gi|86533720|gb|CI173926.1|CI173926
EST:     TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAG                         ATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT
genomic: TACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATT

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), 68 (downstream exon)
Score: 11

TTGAAATCTGCTCTTTTACTTCACATTGACGGATCCACTGCTGTTTCTGAAAATAACGGCCGTCAGgtatggtgaa ... tctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATTGATGCTGTTGACCGTGATACAGTAATGGAAACAGCTAAGGATTTCATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagttgctactatttttcctaactatgtatattccctcgaccatctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATTGATGCTGTTGACCGTGATACAGTAATGGAAACAGCTAAGGATTTCATAA
                  tcctaac  putative branch site (score: 11)
                     taactatgtatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtgaatgaaatattttcttaagtgcccatgttgcagttgctactatttttcctaactatgtatattccctcgaccatctggatcagATGCTAACGTATGGGCGAGTAATGCCATTCTTAGAGCTTTTTGCTCGCATTGATGCTGTTGACCGTGATACAGTAATGGAAACAGCTAAGGATTTCATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT