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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcgaaatcctctcgttttggtattattctgctagttaccattcaaactgaaatatactttagctgattatttctatgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGTACTTCACGTTCAAGAAGGGTGTTGTGAGAGTAGAAACCCAGGGCATTTG

Basic information

species Oryza sativa
transcript LOC_Os08g44370.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G085960_T01 (Zea mays), 3'ss of exon 7
gtatatcgaaatcctctcgttttg-----gtattattctgctagttaccattcaaactga-----aatatactttagctgattatttctatgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGTACTTCACGTTCAAGAAGGGTGTTGTGAGAGTAGAAACCCAGGGCATTTG
|||| |  ||||  |    |  |      ||||  || ||  | |||||||  ||  |||     || | ||||| |   |  |   | || |||| |||||||||||| |||||||||||||||||||||||| |  |||| || ||||||||||| |||||||||||||| |||||||| || ||||||||||||||
gtatctgaaaataataatatactactggtgtatgcttttgtcaattaccatcaaatatgagaagtaacacacttttgacaaaaaccgcaatctgtttagGAATTTTCCTTCATGATCCTGTGAGCTTCACTGCCGTGCTTCATCCCGAGTACTTCACATTCAAGAAGGGTGTGGTGAGAGTGGAGACCCAGGGCATTTG

upper sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G015344_T01 (Zea mays), 3'ss of exon 7
-----gtatatcgaaatcctctcgttttggtattattctgctagttaccattcaaactga-----aatatactt-tagctgattatttctatgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGTACTTCACGTTCAAGAAGGGTGTTGTGAGAGTAGAAACCCAGGGCATTTG
       | ||  | |   |     | |  |||  || ||| | |||||||  ||  |||     || |  ||| |  | ||  ||  || | ||||||||||||||||| |||||||||||||||||||||||| || |||| || ||||||||||| |||||||||||||| ||||||||||| ||||||||||||||
gtatttgaaattaataatatactactgttatatgcttttgccaattaccatcaaatatgagaagaaacacgcttctgacagaaaatcgctttctgttcagGAATTTTCCTTCATGATCCTGTGAGCTTCACTGCCGTACTTCATCCAGAGTACTTCACATTCAAGAAGGGTGTGGTGAGAGTAGAGACCCAGGGCATTTG

upper sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G37830.2 (Glycine max), 3'ss of exon 6
gtatatcgaaatcctctcgttttggtattattctgctagttaccattcaaactgaaatat-actttagc--tgattatttctatgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGTACTTCACGTTCAAGAAGGGTGTTGTGAGAGTAGAAACCCAGGGCATTTG
       | |||  | || || |  |   ||    |||||||   ||| |    |||  |  |  | |   |||| ||||   |   ||||||||||||||||||||||||||| || ||    ||  | || |  || ||    ||||| | ||||||||| || ||||| ||||| || || ||||| ||
-------gtaatt-tttcattctacttcaatgtcactagttatgcttctactaaaaaagttgccatgggaatgatgatttggcttctttcagGAATTTTCCTCCATGATCCTGTCAGTTTTGTGGCAGTTGTGCGTCCAGATCTTTTCACATACAAGAAGGGGGTAGTGAGGGTAGAGACACAAGGCATCTG

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|27920535|gb|CB096343.1|CB096343
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|38471404|gb|CF955535.1|CF955535
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29658032|gb|CB654307.1|CB654307
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCGTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29670960|gb|CB667235.1|CB667235
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29614111|gb|CB619124.1|CB619124
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29614071|gb|CB619084.1|CB619084
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29614027|gb|CB619040.1|CB619040
EST:     CATGTGCCAGTTTTATAGAGACTGGCATGCCGAATCCGATGGCTTTCAGG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29623183|gb|CB628194.1|CB628194
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29614082|gb|CB619095.1|CB619095
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29614023|gb|CB619036.1|CB619036
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|38481551|gb|CF965640.1|CF965640
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGCATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAG
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATG-ATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAG
EST: gi|163920050|gb|EG712004.1|EG712004
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|4716626|gb|AU057742.1|AU057742
EST:     CATGTCCCGGTTCTATAGAGACTGGCATCCCGAATCCCATGGCTTTCATG                         GAATTTCCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29614069|gb|CB619082.1|CB619082
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|58678875|gb|CK067562.1|CK067562
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTT
EST: gi|29614109|gb|CB619122.1|CB619122
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|4716625|gb|AU057741.1|AU057741
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|29614025|gb|CB619038.1|CB619038
EST:     CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: CATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
EST: gi|11564758|gb|AU165394.1|AU165394
EST:     AGTTCTATAGAGA-TGGCATGCCGAATCCGATGGCTTTCATG                         GAATTTTCCCCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT
genomic: AGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGT

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: 60 (upstream exon), 48 (downstream exon)
Score: 31

CTCCTGGAGCTAAGAAACTCAAAAGGGAAGCATGCACAGTTCTTATGTGACATGTGCCAGTTCTATAGAGACTGGCATGCCGAATCCGATGGCTTTCATGgtatatcgaa ... atgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGTACTTCACGTTCAAGAAGGGTGTTGTGAGAGTAGAAACCCAGGGCATTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagttaccattcaaactgaaatatactttagctgattatttctatgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGTACTTCACGTTCAAGAAGGGTGTTGTGAGAGTAGAAACCCAGGGCATTTG
                               agctgat  putative branch site (score: 31)
                                        tttctat  putative PPT
                  tgaaatatacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatcgaaatcctctcgttttggtattattctgctagttaccattcaaactgaaatatactttagctgattatttctatgtgttcagGAATTTTCCTCCATGATCCTGTGAGCTTCACTGCCCTAGTTCACCCTGAGTACTTCACGTTCAAGAAGGGTGTTGTGAGAGTAGAAACCCAGGGCATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG