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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTCGTGGCTGCCGCAGCGCCGGCGGCCGCGGAGGAGGAGAAGGCGAACAAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcaccgcttgcctctctccttcacatgggttctcctgtcgctttcgatttggaactgaactgctgctagatccttgggactggaagcgatcttag...

Basic information

species Oryza sativa
transcript LOC_Os03g61050.1
intron # 1
splice site 5'
intron type U2

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|88344836|gb|CI624487.1|CI624487
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88390343|gb|CI607379.1|CI607379
EST:     AAGTTCCGGCAGCGCGAGGCCAACGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88958940|gb|CI685750.1|CI685750
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88396364|gb|CI598476.1|CI598476
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|58607225|gb|CK035258.1|CK035258
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88407008|gb|CI578536.1|CI578536
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88395082|gb|CI609398.1|CI609398
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88731877|gb|CI753387.1|CI753387
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTACAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88583171|gb|CI700636.1|CI700636
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88431688|gb|CI576879.1|CI576879
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88423838|gb|CI609869.1|CI609869
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88324539|gb|CI568158.1|CI568158
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|58672499|gb|CK061185.1|CK061185
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88376754|gb|CI597734.1|CI597734
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88357480|gb|CI623534.1|CI623534
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88426667|gb|CI579496.1|CI579496
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88316701|gb|CI624143.1|CI624143
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGATATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88388791|gb|CI592679.1|CI592679
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88396846|gb|CI577995.1|CI577995
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88695351|gb|CI737854.1|CI737854
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTA
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTA
EST: gi|13447553|gb|AU181047.1|AU181047
EST:     CAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: CAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88422933|gb|CI615233.1|CI615233
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTC-AAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|7378442|gb|AU088713.1|AU088713
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88363740|gb|CI609097.1|CI609097
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88390242|gb|CI605695.1|CI605695
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAAAATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88362332|gb|CI608723.1|CI608723
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88350368|gb|CI623306.1|CI623306
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88359727|gb|CI622417.1|CI622417
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|5607636|gb|AU076308.1|AU076308
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88720974|gb|CI744273.1|CI744273
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
EST: gi|88417906|gb|CI596583.1|CI596583
EST:     AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCT                         TGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG
genomic: AAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAG

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: 68 (upstream exon), 75 (downstream exon)
Score: 13

TTCTCGTGGCTGCCGCAGCGCCGGCGGCCGCGGAGGAGGAGAAGGCGAACAAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcacc ... ttctccgcagTGATGAAGATGCTTTATTGAAGACCAAGTGTCCAAAACATGTAGAGCTGAGATGGCAGACTGAAGTTAGTTCCAGCATTTATGCAACTCCGTTGATCGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTCGTGGCTGCCGCAGCGCCGGCGGCCGCGGAGGAGGAGAAGGCGAACAAGTTCCGGCAGCGCGAGGCCACCGACGACATGCTTGGATACCCCCACCTgtgagtcaccgcttgcctctctccttcacatgggttctcctgtcgctttcgatttggaactgaactgctgctagatccttgggactggaagcgatcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc