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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgcagtgctattatattaaggggtgaatgacagcagaatgtggaatgctttaagagcaatcctttgccaattcactgacgtatgcttcatatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTCTGAGCGGAGAGCGCTGATGGGCGAATCAAGTGAT

Basic information

species Oryza sativa
transcript LOC_Os01g62420.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 3
actgcagtgctattatattaaggggtgaatgacagcagaatgtggaatgctt-taagagcaatcctttgccaattcactgacgtatgc----ttcatatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTCTGAGCGGAGAGCGCTGATGGGCGAATCAAGTGAT
                            ||   ||      ||| |||  |     ||| | | |||  |||||| ||| |  | ||     ||  |  || |||||| |||||| |||| |||||||||||||| ||||| ||| ||||||| |||||||| ||||| ||| |||| ||||| ||||||
----------------------------atccaagtcactagtgaaataataactggagtatttctt--ccaattgactaatatgtgtcagttttcttgtttcagtgctgagatgctggtaaacctgcagGTGCCCTGGGTCATTTTGGGACATTCTGAGCGCAGAGCTCTGTTGGGTGAATCCAGTGAT

upper sequence: LOC_Os01g62420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G146206_T04 (Zea mays), 3'ss of exon 3
actgcagtgctattatattaaggggtgaatgacagcagaatgtggaatgctt-taagagcaatcctttgccaattcactgacgtatgc----ttcatatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTCTGAGCGGAGAGCGCTGATGGGCGAATCAAGTGAT
|   |  |  |  | ||||     ||  ||   ||      ||| |||  |     ||| | | |||  |||||| ||| |  | ||     ||  |  || |||||| |||||| |||| |||||||||||||| ||||| ||| ||||||| |||||||| ||||| ||| |||| ||||| ||||||
atgtccatagtgctctattt---cgttgatccaagtcactagtgaaataataactggagtatttctt--ccaattgactaatatgtgtcagttttcttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTCTGAGCGCAGAGCTCTGTTGGGTGAATCCAGTGAT
















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|27576926|gb|CA999620.1|CA999620
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|33689962|gb|CF318201.1|CF318201
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGGTGAT-CTGGGACACT
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGG-TGATTCTGGGACACT
EST: gi|33688031|gb|CF316270.1|CF316270
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|33688122|gb|CF316361.1|CF316361
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|58597190|gb|CK007718.1|CK007718
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATACTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|33809786|gb|CF330782.1|CF330782
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGCGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|33689921|gb|CF318160.1|CF318160
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|33693382|gb|CF321621.1|CF321621
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|58682138|gb|CK070825.1|CK070825
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTNGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgctttaagagcaatcctttgccaattcactgacgtatgcttcatatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTCTGAGCGGAGAGCGCTGATGGGCGAATCAAGTGAT
                             cactgac  putative branch site (score: 2)
                                          ttcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgcagtgctattatattaaggggtgaatgacagcagaatgtggaatgctttaagagcaatcctttgccaattcactgacgtatgcttcatatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTCTGAGCGGAGAGCGCTGATGGGCGAATCAAGTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
-ctgcagt
- - - - - - - - - - - - gtgaatg
- - - - - - - - - - - - - - - - cagcaga
- - - - - - - - - - - - - - - - - - - - - -ggaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -aagagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcttc