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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagggattgtatcttcgtgagaaattagttttgatttcgttggtgtttttgctgctgctgctttatttttttccctgataaccgtatggattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG

Basic information

species Oryza sativa
transcript LOC_Os07g43060.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g43060.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G086805_T01 (Zea mays), 3'ss of exon 1
---tttagggattgtatcttcgtgagaaatt--agttttgatttcgttggtgtttttgctgctgctgctttatttttttccctgataaccgtatggattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG
   |||    |||| ||     |   || ||  ||| |||||  || ||||| |     ||||   || ||   ||  |   ||      | |||   ||  ||||||| |||| | |||||||| |||||||| || || || ||||| || || |||||||||||||||||||||||||||||||||||||| ||
gtgttttatcattgaattcctattgcaagttgtagtgttgatgccgatggtggtccgcatgctcacgcgtttaattgctgtttgg-----ggatgctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG
















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|55431292|gb|CV728660.1|CV728660
EST:     ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
EST: gi|11610378|gb|AU166054.1|AU166054
EST:     ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
EST: gi|58686363|gb|CK075050.1|CK075050
EST:     ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
EST: gi|88833830|gb|CI077311.1|CI077311
EST:     ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
EST: gi|86423375|gb|CI060948.1|CI060948
EST:     GCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: GCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
EST: gi|8857385|gb|AU094703.1|AU094703
EST:     ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
EST: gi|163919996|gb|EG709802.1|EG709802
EST:     ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
EST: gi|163928022|gb|EG709470.1|EG709470
EST:     ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
EST: gi|87019382|gb|CI279892.1|CI279892
EST:     GCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: GCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
EST: gi|88976243|gb|CI024460.1|CI024460
EST:     ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAG                         TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT
genomic: ACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccg ... gattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttgctgctgctgctttatttttttccctgataaccgtatggattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG
                                tgataac  putative branch site (score: 2)
               tgctttattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagggattgtatcttcgtgagaaattagttttgatttcgttggtgtttttgctgctgctgctttatttttttccctgataaccgtatggattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG

- - - - - - - cttcgtg
- - - - - - - - - - - - - - - - - - - - gttggtg
- - - - - - - - - - - - - - - - - - - - - - - - -tttgctg