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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagacatttctgcatgggcgcaacaagaatgtgctgtgtagctcttgtttgatcgtcttatttcagtgagttctttgctgactagttatattggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAGATTACGTTTATCAAAGAATCAGCTTCTAACTATTCCACTCTGGCAAAGG

Basic information

species Oryza sativa
transcript LOC_Os01g18070.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G140885_T02 (Zea mays), 3'ss of exon 3
tagacatttctgcatgg--gcgcaacaagaatgtgctgtgtagctcttgtttgatcgtcttatttcagtgagttctttgctgacta-gttatattggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAGATTACGTTTATCAAAGAATCAGCTTCTAACTATTCCACTCTGGCAAAGG
   |  |   ||  |||  | | ||| ||||| || ||   ||  |||||||| |  |||||||||  ||  | ||||  |||||  | | | ||||||| ||||||||||||| |||||||||||||| |||||||||||||| |||||||||||  | |||||||  ||||||||||| |||||||||| |||| | ||||
acaatgtccatgggtggaagtggaacgagaatatgttgcagaggccttgtttggt-atcttatttc--tgcatgctttcatgactctgctctgttggatttagGTATGGGGAGGGAACCCTGCCAAATTTCTGAGGAAGCTCACAGATGACGAGATCGCATTTATCACGGAATCAGCTTCCAACTATTCCAATCTGTCCAAGG

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G046924_T02 (Zea mays), 3'ss of exon 4
tagacatttctgcatggg---cgcaacaagaatgtgctgtgtagctcttgtttgatcgtcttatttcagtgagttctttgctgacta-gttatattggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAGATTACGTTTATCAAAGAATCAGCTTCTAACTATTCCACTCTGGCAAAGG
|||   |   ||  ||||    | ||||| ||| |||| |  ||  |||||||  |  |||||||||  ||  |  |||  |||||| | | | ||||||| ||||||||||||| |||||||||||||| |||||||||||||| ||||||||||| |  || ||    ||||||||| | |||||||||| |||| | ||||
tag-tgtccatgagtgggaagtggaacaataatatgctctagaggccttgttttgt-atcttatttc--tgcatgatttcatgactatgctttgttggatttagGTATGGGGAGGGAACCCTGCCAAATTTCTGAGGAAGCTCACAGATGACGAGATCAGTTTCATTGCGGAATCAGCTGCCAACTATTCCAATCTGTCCAAGG

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G19580.2 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------tagacatttctgcatgggcgcaacaagaatgtgctgtg----tagctcttgtttgatc-gtcttatt---tcagtgagttc---tttgctgactagt-tatattggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAGATTACGTTTATCAAAGAATCAGCTTCTAACTATTCCACTCTGGCAAAGG
                                             |  | ||   |||    | |    |           ||    ||    ||  || ||| | | ||||   | |  |||||    | | |  | | || |||| || | ||||||||||||||||||||| || |  ||||| ||||||||||||||||| || ||| | ||||||    | |||||  | ||||| || |  || ||| |||
gttagttagatgaaagtggaaatgttcttctagctatggtttatctgcatatgaatgccaaagggtgttagtctctcatcatggccttaaaatttacttcatccgccatattgactgacagagttaaaatgttcgcattggtctataatg-actcagGTATGGGGAGGAAACCCAGCAAGGTTCCTCAGGAAGCTCACTGATGAGGAAATTGCTTTTATCTCTCAGTCAGCAACAAACTACTCAAACCTCGCACAGG

upper sequence: LOC_Os01g18070.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G19580.1 (Arabidopsis thaliana), 3'ss of exon 4
--tagacatttctgcatgggcgcaacaagaatgtgctgtgtagctcttgtttgatcgtcttatttcagtgagttctttgctgactagt-tatattggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAGATTACGTTTATCAAAGAATCAGCTTCTAACTATTCCACTCTGGCAAAGG
   | |   |  |       |   |      |    | |    |    |    || | || |      | |  | || ||  | | || |||| || | ||||||||||||||||||||| || |  ||||| ||||||||||||||||| || ||| | ||||||    | |||||  | ||||| || |  || ||| |||
gccaaagggtgttagtctctcatcatggccttaaaatttacttcatccgccatattgactgacagagttaaaatgttcgc--attggtctataatg-actcagGTATGGGGAGGAAACCCAGCAAGGTTCCTCAGGAAGCTCACTGATGAGGAAATTGCTTTTATCTCTCAGTCAGCAACAAACTACTCAAACCTCGCACAGG

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|86499355|gb|CI141988.1|CI141988
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|88985994|gb|CI033323.1|CI033323
EST:     GCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: GCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|89189074|gb|CI012224.1|CI012224
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|58606849|gb|CK034882.1|CK034882
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|87016255|gb|CI271666.1|CI271666
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGGGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|3763551|gb|AU030303.1|AU030303
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|87025510|gb|CI267876.1|CI267876
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|29667595|gb|CB663870.1|CB663870
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|88238735|gb|CI238584.1|CI238584
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|86507238|gb|CI149871.1|CI149871
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGAAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|3766564|gb|AU030674.1|AU030674
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|163927400|gb|EG713864.1|EG713864
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|88844391|gb|CI005764.1|CI005764
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|88241861|gb|CI241710.1|CI241710
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|88206266|gb|CI206115.1|CI206115
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|313079509|gb|HO213067.1|HO213067
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|86834698|gb|CI340815.1|CI340815
EST:     AAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTCCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: AAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|86875970|gb|CI325529.1|CI325529
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTTCCAAATTCCTGAGGAAGCTCACCTGATGACGA
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCA-CTGATGACGA
EST: gi|89182736|gb|CI114105.1|CI114105
EST:     TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: TTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
EST: gi|88207363|gb|CI207212.1|CI207212
EST:     AGGATCCCCTGTGGAGAG                         GTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG
genomic: AGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 75 (downstream exon)
Score: 75

TATGGGGGCGACCCTGTTAGATGGTGTTGTCGTGGAAAAGCATGGGATGGTTGCTGCTGGAGCCCTTGTAAGACAGAACACAAGGATCCCCTGTGGAGAGgttgtgcatt ... ttggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAGATTACGTTTATCAAAGAATCAGCTTCTAACTATTCCACTCTGGCAAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgatcgtcttatttcagtgagttctttgctgactagttatattggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAGATTACGTTTATCAAAGAATCAGCTTCTAACTATTCCACTCTGGCAAAGG
                              tgctgac  putative branch site (score: 75)
                                     tagttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagacatttctgcatgggcgcaacaagaatgtgctgtgtagctcttgtttgatcgtcttatttcagtgagttctttgctgactagttatattggattcagGTATGGGGAGGAAACCCTGCCAAATTCCTGAGGAAGCTCACTGATGACGAGATTACGTTTATCAAAGAATCAGCTTCTAACTATTCCACTCTGGCAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - tgcatgg
- - - - - - - - - - caacaag
- - - - - - - - - - - - - - - gtgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgac