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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGACTGATGGTGCTGTCCTTGTGAACGGAAATGATACCGAGGAACAGTGGGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcctaaaaccctttttttggtcctcgtttatcctcccagtgcaccaatgatcacaatgaaaacttgatgctggtgtcctcaaaaagaaagaaag...

Basic information

species Oryza sativa
transcript LOC_Os02g11840.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 24
TCGACTGATGGTGCTGTCCTTGTGAACGGAAATGATACCGAGGAACAGTGGGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcctaaaaccctttttttggtcctcgtttatcctcccagtgcacca-atgatcacaat--gaaaacttgatgctggtgtcctcaaaaagaaagaaag
|| ||||||||||||||||||||||| |||||  |||  |||||||||||||||| ||| || |||||| |||||||||||||||||||||||||||||||||||||||||||  |||| ||||  |||| || |  ||||||||||||| | || |  | |    |   |  |  |   | || |||       |  |  | 
TCAACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGGTATGAAAAATGAAGAACCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcctaaataccttatttt--tcctggtcttacctcccagtgcacgatattaggaaagctgggtgatatccttaagttgcccttgtctttagcggta-

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 24
------------------------------------------------TCGACTGATGGTGCTGTCCTTGTGAACGGAAATGATACCGAGGAACAGTGGGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcctaaaaccctttttttggtcctcgtttatcctcccagtgcaccaatgatcacaatgaaaacttgatgctggtgtcctcaaaaagaaagaaag
                                                || ||||||||||||||||||||||| |||||  |||  |||||||||||||||| ||| || |||||| |||||||||||||||||||||||||||||||||||||||||||  |||| ||||  |||| || |  |||||||||||||  ||                                              
GGAGTAGAAGAAAGTCAGGATGAAGCTGTTGAGGTTGAGGCTGAGGATTCAACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaatgaagaaccatcagcataaaagctgtagttgagcaagtgtacagtcctaaataccttatttt--tcctggtcttacctcccagtgcac-gata---------------------------------------------

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 24
------------------------------------------------TCGACTGATGGTGCTGTCCTTGTGAACGGAAATGATACCGAGGAACAGTGGGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcctaaaaccctttttttggtcctcgtttatcctcccagtgcaccaatgatcacaatgaaaacttgatgctggtgtcctcaaaaagaaagaaag
                                                || | ||||||||||||||||||||| |||||   || ||||||||||||||||||||| || |||||| |||||||||||||||||||||||||||||||||||||||||||  |||| ||||   ||| || |  ||||| ||| |||  ||                                              
GGAGTAGAAGAAAGTCAAGATGAAGCTGTTGAGGTTGAGGCTGAGGGTTCAAGTGATGGTGCTGTCCTTGTGAATGGAAACAGTAGCGAGGAACAGTGGGgtacgaaaaatgaagaaccatcagcataaaagctgtagttgagcaagtgtacagtcctaaataccttatttt---cctggtcttacctccaagtacac-gatat--------------------------------------------

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 24
TCGACTGATGGTGCTGTCCTTGTGAACGGAAATGATACCGAGGAACAGTGGGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcctaaaaccctttttttggtcctcgtttatcctcccagtgcaccaatgatcacaatgaaaacttgatgctggtgtcctcaaaaagaaagaaag----
|| | ||||||||||||||||||||| |||||   || ||||||||||||||||||||| || |||||| |||||||||||||||||||||||||||||||||||||||||||  |||| ||||   ||| || |  ||||| ||| ||| |        ||      || | || |  | | ||  | |       |||    
TCAAGTGATGGTGCTGTCCTTGTGAATGGAAACAGTAGCGAGGAACAGTGGGGTACGAAAAATGAAGAACCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcctaaataccttatttt---cctggtcttacctccaagtacacgatattaggaaactcctgctgggtgatc-tattctggatatatccttaagttgc

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|88965746|gb|CI006623.1|CI006623
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|87021442|gb|CI274049.1|CI274049
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|29644063|gb|CB649070.1|CB649070
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|33800696|gb|CF326218.1|CF326218
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|87021165|gb|CI271972.1|CI271972
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|86480883|gb|CI123516.1|CI123516
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|86481559|gb|CI124192.1|CI124192
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|86478917|gb|CI121550.1|CI121550
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|88461084|gb|CI550247.1|CI550247
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|86521390|gb|CI161596.1|CI161596
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|88267615|gb|CI379550.1|CI379550
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGATCAAGT                         TATTGACTCCTGACCAATAGTTAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|86886937|gb|CI324358.1|CI324358
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
EST: gi|86477288|gb|CI119921.1|CI119921
EST:     GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGT                         TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG
genomic: GGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcct ... ccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGACTGATGGTGCTGTCCTTGTGAACGGAAATGATACCGAGGAACAGTGGGGTACGAACAACGAAGAATCATCAGCATAAAAGCTGTAGTTGAGCAAGTgtacagtcctaaaaccctttttttggtcctcgtttatcctcccagtgcaccaatgatcacaatgaaaacttgatgctggtgtcctcaaaaagaaagaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa