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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCTGCTGTTGGCGGCTGAATCACGAGCTGAGAAAGCAAAGAAAGGAGTTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcactcttgcttgttcttttacttttacttttcctttggcacctttattaactcgtagttcctatgcgctcag

Basic information

species Oryza sativa
transcript LOC_Os02g32350.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AC207890.3_FGT002 (Zea mays), 5'ss of exon 10
TGACCTGCTGTTGGCGGCTGAATCACGAGCTGAGAAAGCAAAGAAAGGAGTTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcactcttgcttgttcttttacttttacttttcctttggcacctttattaactc---gtagttcctatgcgctcag
|||     | || || ||||||||||| |||||||||||||||||||| || ||||||   |||||||| ||||| ||||| |||||||| || ||||| ||   |   | || |      ||| | ||| |  ||| ||    || | |||     ||   || || | |    ||  ||
TGATGCTTTATTAGCAGCTGAATCACGCGCTGAGAAAGCAAAGAAAGGCGTGCATTCTCAGAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgta-agtgatgtttccgtcaatttgattttgatattttctgcatcatcattaacctatcagtgtggtccttgcatgcatag

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G136296_T01 (Zea mays), 5'ss of exon 11
TGACCTGCTGTTGGCGGCTGAATCACGAGCTGAGAAAGCAAAGAAAGGAGTTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcactcttgcttgttcttttacttttactttt---cctttggcacctttattaactc------gtagttcctatgcgctcag
|||    || || || ||||||||||| ||||||||||||||||||||||| ||||||  ||||||||| ||||| ||||| |||||||| || ||||| ||  |  |   |   || |||  | | ||  | |||       |  ||  | | ||||||        || || | |||  |   ||
TGATGCTCTATTAGCAGCTGAATCACGGGCTGAGAAAGCAAAGAAAGGAGTGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgatattcatttattccatcagttcgattttgatattctctgcgtcatcattaacctatcagtgtggtccttatatggatag

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT5G07350.1 (Arabidopsis thaliana), 5'ss of exon 11
TGACCTGCTGTTGGCGGCTGAATCACGAGCTGAGAAAGCAAAGAAAGGAGTTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttg-gcactcttgcttgttcttttacttttacttttcctttggcacctttattaactcgtagttcctatgcgctcag----------------------------
|||    ||  |||| |||||| | || |||  |   | |||||||||| | ||||||||||||||||| || | ||||||||| |||||| | ||   |||| |   |    |   | |   | ||  | | | | | | |    | |    ||  ||| |    | | |   || |                             
TGATGCTCTTCTGGCTGCTGAAGCTCGTGCTCTGGCTGGAAAGAAAGGAATCCATTCTGCAAAAGAATCTCCAGCCATGCACATCACAGACCTAACTGTGgttagtatatatatatatatatatatatatctccatgtacataataaacgcattttcctcattaacctttttgactaatctaatgtgtaaccatatatttgtctcag

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|88392637|gb|CI625459.1|CI625459
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGC
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGC
EST: gi|218501667|gb|FG956183.1|FG956183
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|29622581|gb|CB627592.1|CB627592
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|29674464|gb|CB670739.1|CB670739
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|33795444|gb|CF323592.1|CF323592
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|33793429|gb|CF322594.1|CF322594
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|29623578|gb|CB628589.1|CB628589
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|88352099|gb|CI626099.1|CI626099
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTT
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTT
EST: gi|33796827|gb|CF324278.1|CF324278
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|33795788|gb|CF323763.1|CF323763
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|29627293|gb|CB632304.1|CB632304
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|25800307|gb|CA756268.1|CA756268
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|218500523|gb|FG958817.1|FG958817
EST:     CCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: CCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|58679279|gb|CK067966.1|CK067966
EST:     TTCATTCTGCAAAAGAAGCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGGCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|29644259|gb|CB649266.1|CB649266
EST:     TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
EST: gi|58692787|gb|CK081474.1|CK081474
EST:     -TCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACG                         GTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA
genomic: TTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcact ... atgcgctcagGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACCTGCTGTTGGCGGCTGAATCACGAGCTGAGAAAGCAAAGAAAGGAGTTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcactcttgcttgttcttttacttttacttttcctttggcacctttattaactcgtagttcctatgcgctcag

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