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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttcaaactacctatctagttttaattcaaaattttccatgcatttctcaaaaaaatttatggtcatggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCGAAAGGATTGAGTTCTACAAGAACTACCTCACTGAACTGAAGAAAGCCAT

Basic information

species Oryza sativa
transcript LOC_Os03g49610.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49610.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AC217401.3_FGT002 (Zea mays), 3'ss of exon 10
------------------------------gtattttcaaactacctatc-tagttttaattcaaaattttccatgcatttctcaaaaaaatttatggtcatggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCGAAAGGATTGAGTTCTACAAGAACTACCTCACTGAACTGAAGAAAGCCAT
                                ||  |   ||| |||  | | ||  |  || ||     || | | ||         |    |||  | |   || |||||||||||||  ||||||| ||||| || || |||| | |||| ||| |||  ||||| || ||||||||||||||||| || || || |||| ||  ||
gtacctgaaataacctgtttccttcgtctgaaatgcttgcactcccttccatggtgctccttgaaccgcatcaacgaatcatggctccatgaatataataa--atatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCGTGAGGATCGACTTCTACAAGAACTACCTGACGGAGCTAAAGAGAGGGAT
















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|58682297|gb|CK070984.1|CK070984
EST:     ATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: ATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|27554361|gb|CA998261.1|CA998261
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58669788|gb|CK058474.1|CK058474
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58673908|gb|CK062594.1|CK062594
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58660033|gb|CK048713.1|CK048713
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|163925553|gb|EG715398.1|EG715398
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58674306|gb|CK062992.1|CK062992
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58674546|gb|CK063233.1|CK063233
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58671067|gb|CK059753.1|CK059753
EST:     GGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: GGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58604470|gb|CK014998.1|CK014998
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAG
EST: gi|58597512|gb|CK008040.1|CK008040
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GCATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58598545|gb|CK009073.1|CK009073
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGAC
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGAC
EST: gi|58668081|gb|CK056767.1|CK056767
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|33676240|gb|CF304479.1|CF304479
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|33684008|gb|CF312247.1|CF312247
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|38481806|gb|CF965877.1|CF965877
EST:     TAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: TAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|27554359|gb|CA998259.1|CA998259
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58683577|gb|CK072264.1|CK072264
EST:     ATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: ATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
EST: gi|58671037|gb|CK059723.1|CK059723
EST:     CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATG                         GAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG
genomic: CTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCG

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: 58 (upstream exon), 66 (downstream exon)
Score: 12

AACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTGAACTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAAATGgtattttcaa ... atggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCGAAAGGATTGAGTTCTACAAGAACTACCTCACTGAACTGAAGAAAGCCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaattcaaaattttccatgcatttctcaaaaaaatttatggtcatggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCGAAAGGATTGAGTTCTACAAGAACTACCTCACTGAACTGAAGAAAGCCAT
 ttttaat  putative branch site (score: 12)
                      atttctcaaaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttcaaactacctatctagttttaattcaaaattttccatgcatttctcaaaaaaatttatggtcatggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCGAAAGGATTGAGTTCTACAAGAACTACCTCACTGAACTGAAGAAAGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA