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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggcttcaccctccgtagcaaaaatttgccaacattatcttacctacctgtctgccaacttctgttttcctgacgtgctaagggatgttagaaatttcctcatcaatattagtttcagacaaatttgtgtgaggttggttacctatcagatgaaattatctgatcaagctcattgtttatgtatgccag

Basic information

species Oryza sativa
transcript LOC_Os07g16970.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 2
GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggcttcaccctccgtagcaaaaatttgccaacattatcttacctacctgtctgccaacttctgttttcctgacgtgctaagggatgttagaaatttcctcatcaatattagtttcagacaaatttgtgtgaggttggttacctatcagatgaaattatctgatcaagctcattgtttatgtatgccag
||| |||| |||||||||||||| |||||||| |||||||||||||||||||| || ||||||||||||| ||    |          | |  | ||    |  ||| ||       || ||  |  |     |||  |||| ||  |  |  |||            ||    | | | |  |                                                                          
GTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTCAATCTCAATCAGgtgacaatgcaaggctg--------atatgtctgttggcgatattttg---gagtgcct--cgcccctcatttctctgaggttgtgggtaatggcga--------tccatgagactcgcct--------------------------------------------------------------------------
















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|29624786|gb|CB629797.1|CB629797
EST:     ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAG                         CTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
genomic: ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
EST: gi|88735266|gb|CI758774.1|CI758774
EST:     ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAG                         CTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
genomic: ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
EST: gi|88408099|gb|CI601577.1|CI601577
EST:     ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAG                         CTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
genomic: ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
EST: gi|88735048|gb|CI758556.1|CI758556
EST:     ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAG                         CTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
genomic: ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
EST: gi|29616692|gb|CB621704.1|CB621704
EST:     ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAG                         CTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
genomic: ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
EST: gi|88407824|gb|CI588853.1|CI588853
EST:     ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAG                         CTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
genomic: ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
EST: gi|88744533|gb|CI767893.1|CI767893
EST:     ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAG                         CTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
genomic: ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
EST: gi|58692091|gb|CK080778.1|CK080778
EST:     ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAG                         CTATGGAACAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
genomic: ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
EST: gi|58655667|gb|CK044347.1|CK044347
EST:     CTACGGTGGAGACTCCACATCGCTCAA-CTGAATCAG                         CTATGGAAAAGGTTCAAAGGTGAAGGTACGCGGCCGGCGCAAATTGGGGCT
genomic: CTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
EST: gi|88407852|gb|CI588881.1|CI588881
EST:     ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAG                         CTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT
genomic: ACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCT

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: 63 (upstream exon), 75 (downstream exon)
Score: 18

GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggc ... tgtatgccagCTATGGAAAAGGTTCAAAGGTGAAGGTACTCCCCCGGCGCAAATTGGGGCTAGCAGAGACTACAATGTAGACATGATTCCAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTGCATATGGACAGGAATGATTACTACGGTGGAGACTCCACATCGCTCAACCTGAATCAGgtgacaaggcttcaccctccgtagcaaaaatttgccaacattatcttacctacctgtctgccaacttctgttttcctgacgtgctaagggatgttagaaatttcctcatcaatattagtttcagacaaatttgtgtgaggttggttacctatcagatgaaattatctgatcaagctcattgtttatgtatgccag

- - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - TGGAGA