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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGCACAGAATGTGGAAAGCTCCCAGTGCATCACAATGTTGGAAGCTGTAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatattgtcctttaacctcagcttcttcgtatttttcttagattgcaggctatagagtttgtattgattattgagtaatcttcacctagtactaat...

Basic information

species Oryza sativa
transcript LOC_Os09g31970.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g31970.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G001645_T01 (Zea mays), 5'ss of exon 3
TCCTGCACAGAATGTGGAAAGCTCCCAGTGCATCACAATGTTGGAAGCTGTAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatattgtcctttaacctcagcttcttcgtatttttcttagattgca-ggctatagagtttgtattgattattgagtaatcttcacctagt-actaat-
 ||||||||||| ||||| || |||||||||||||| |||||||||||| ||||||||||||||||||| || |||||||||||||||||||| |||||||| ||  |   |||| |   || |   | || |   ||       |||  | ||   |  |   | |  ||   ||    |  |    ||||||| | | || 
CCCTGCACAGAACGTGGAGAGTTCCCAGTGCATCACCATGTTGGAAGCTATAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgt-ttgaaacatcctatg--ctaatgatgtttgctcttccacggaattttatggtccttaataatttggtgtccataagttttttaagacctagtgattgatt

upper sequence: LOC_Os09g31970.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G058095_T02 (Zea mays), 5'ss of exon 2
TCCTGCACAGAATGTGGAAAGCTCCCAGTGCATCACAATGTTGGAAGCTGTAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatattgtcctttaacctcagcttcttcgtatttttcttagattgcaggctatagagtttgtattgattattgagtaatcttcacctagt-actaat--
 ||||||||||| ||||| || |||||||| ||||| |||||||||||| ||||||||||||||||||| ||  |||| |||||||||||||| |||||||| ||  |   |||| |          | ||  ||||   |   ||||   ||      |   | |   |   ||    |  |     | |||| | | ||  
CCCTGCACAGAACGTGGAGAGTTCCCAGTGTATCACCATGTTGGAAGCTATAAATGATGGCAAAGATCTGCACGTCTCCGTTACTATGCCATCTATTGAGgt-ttgaaacatcctatgttgatgatgttttactattcgcc--ggatttatggtccctaataatttggcgtccatgatttttttaaggcatagtgattgattg

upper sequence: LOC_Os09g31970.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S139_2V6.1 (Physcomitrella patens), 5'ss of exon 3
TCCTGCACAGAATGTGGAAAGCTCCCAGTGCATCACAATGTTGGAAGCTGTAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatattgtcctttaacctcagcttcttcgtatttttcttagattgcaggctatagagtttg-tattgattattgagtaatcttcacctagtactaat-------------------
|||||||||||| || || ||||| || || || || ||| |||| ||||| |||| |||  ||||| | ||| |||||||||| ||||| |||||||||||||    |||   |||    || |       |  | ||||   || |  |   | |    |    | || | | || |  | | |   |||   ||| |                    
TCCTGCACAGAACGTCGAGAGCTCACAATGTATAACCATGATGGAGGCTGTCAATGGTGGTCAAGATTTACATGTCTCTGTTACGATGCCTTCAATTGAGgtatgcatttgattttt---ttctggacggatgcctgtttcacggagtagaacttgtcctatcccctctttagtctttacaactttcaccctcagactgactgttaaatttcttctgcag

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|396941127|gb|HO188336.1|HO188336
EST:     TAAATGATGGCAAAGATCTTCATATCTCCGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|88243397|gb|CI244519.1|CI244519
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|8594840|gb|AU093378.1|AU093378
EST:     GTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGAAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: GTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|29638806|gb|CB643815.1|CB643815
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|218499333|gb|FG949280.1|FG949280
EST:     TAAATGATGGCAAAGATCTTCATATCTCCGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|218489098|gb|FG949712.1|FG949712
EST:     TAAATGATGGCAAAGATCTTCATATCTCCGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|86488855|gb|CI131488.1|CI131488
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACCATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|87009979|gb|CI277480.1|CI277480
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|87026089|gb|CI250105.1|CI250105
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|88577750|gb|CI674358.1|CI674358
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|86504280|gb|CI146913.1|CI146913
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|29674292|gb|CB670567.1|CB670567
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|89169964|gb|CI039241.1|CI039241
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|58667229|gb|CK055915.1|CK055915
EST:     TAAATGATGGCAAAGATCTTCATATCTCCGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|88344356|gb|CI677394.1|CI677394
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|218486101|gb|FG952696.1|FG952696
EST:     TAAATGATGGCAAAGATCTTCATATCTCCGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|89192976|gb|CI050274.1|CI050274
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|89184185|gb|CI046750.1|CI046750
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|55408271|gb|CV720647.1|CV720647
EST:     TAAATGATGGCAAAGATCTTCATATCTCCGTTACTATGCCATCAATTGAG                         GTGGTCTCGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|86908142|gb|CI300644.1|CI300644
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|88225016|gb|CI224932.1|CI224932
EST:     TAAATGATGGCAAAGATGTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|86492324|gb|CI134957.1|CI134957
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
EST: gi|86414947|gb|CI069350.1|CI069350
EST:     TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAG                         GTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG
genomic: TAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTG

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: 75 (upstream exon), 75 (downstream exon)
Score: 41

TCCTGCACAGAATGTGGAAAGCTCCCAGTGCATCACAATGTTGGAAGCTGTAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatatt ... caaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTGGACCTACTTGGCGTGAAGGGCGCAAACAGGGAATCCCCAGGATCAAATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGCACAGAATGTGGAAAGCTCCCAGTGCATCACAATGTTGGAAGCTGTAAATGATGGCAAAGATCTTCATATCTCTGTTACTATGCCATCAATTGAGgtattatattgtcctttaacctcagcttcttcgtatttttcttagattgcaggctatagagtttgtattgattattgagtaatcttcacctagtactaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG