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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGAATACAAATATATAGTGGACGGCAAATGGGTGTGCAATGACAATGAGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttacttcccagctccctagttccctgtatctgtggacgtgttggataggataacgtaacttgacgtcttcattgcag

Basic information

species Oryza sativa
transcript LOC_Os03g01750.4
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01750.7 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G052546_T05 (Zea mays), 5'ss of exon 1
GTATGAATACAAATATATAGTGGACGGCAAATGGGTGTGCAATGACAATGAGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttacttcccagctccctagttccctgtatctgtggacgtgttggataggataacgtaacttgacgtcttcattgcag
|||||||||||||||  ||||||| ||||||||| | ||||| ||  |||||  ||  || ||| | |||||||| ||||| ||||| ||||| || |||||||| | | |||   | |   |  |   ||   |  | |  | |  || |  ||   |     ||    ||||   |||||
GTATGAATACAAATACGTAGTGGATGGCAAATGGCTATGCAACGAGCATGAGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagat-cctcctgtcccgtcaaatggatg---ccatagctgag--ggctgagagtgcacgcgtt--tttcttggctgcag
















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|88688614|gb|CI732190.1|CI732190
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|29640153|gb|CB645162.1|CB645162
EST:     AGAAGAAGGCCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|24208785|gb|AU225812.1|AU225812
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|29656092|gb|CB652367.1|CB652367
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88688617|gb|CI732193.1|CI732193
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88311093|gb|CI658006.1|CI658006
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|58688312|gb|CK076999.1|CK076999
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCA
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCA
EST: gi|88689968|gb|CI734047.1|CI734047
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88693785|gb|CI735362.1|CI735362
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|2428616|gb|C73079.1|C73079
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATACCTACGTCCAG                         GTCTCCAGGGATGGTACCANCGATGAAGAGNGAGA-TTAAGGGN-CGTTT-
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|87007869|gb|CI296847.1|CI296847
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|29626840|gb|CB631851.1|CB631851
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88690033|gb|CI734112.1|CI734112
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88689057|gb|CI732633.1|CI732633
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|58696174|gb|CK084861.1|CK084861
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|58694687|gb|CK083374.1|CK083374
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88963923|gb|CI031256.1|CI031256
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|27549021|gb|CA767031.2|CA767031
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88688572|gb|CI732148.1|CI732148
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|29656147|gb|CB652422.1|CB652422
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
EST: gi|88689587|gb|CI733163.1|CI733163
EST:     AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAG                         GTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG
genomic: AGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttact ... ttcattgcagGTCTCCAGGGATGGTACCAGCGATGAAGAGAGAGAATTAAGGGAGCGTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGAATACAAATATATAGTGGACGGCAAATGGGTGTGCAATGACAATGAGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttacttcccagctccctagttccctgtatctgtggacgtgttggataggataacgtaacttgacgtcttcattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT