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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatttaattgatggaattaagtttgaaatgccatctccttgtttgttcactactgttattaacaaaataatcattcatcatattgactggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAAGACCATCATCATGTGGAATCTGTACTGCATTCAGCAAAGAATGAATATG

Basic information

species Oryza sativa
transcript LOC_Os01g46980.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46980.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G030167_T01 (Zea mays), 3'ss of exon 3
-tcaatttaattgatggaattaagtttgaaatgccat-ctccttgtttgttcactactgttattaacaaaataatcattcatcatattgactggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAAGACCATCATCATGTGGAATCTGTACTGCATTCAGCAAAGAATGAATATG
 |   ||| ||        || |||  |       || ||   ||    ||||  ||| || |   || |  | | | |||   | ||   |  |||| ||||||||||| || |||||||||||||| ||| | |||||||||||||| || || || |||||||||||||| || ||||||||||||||| |||| ||||
ttttttttgatgtcaaatgttcagtagggccaaatatgctatgtgccatttcagaact-ttctgcgcacatcagttagtcactttgtttgatc-aaatccagGGTTTGCTCCGTTTGAAAGAGCCAGCAGTATTGCTCCGTTGCCGCAAGGATGATCACCATCATGTGGAATCAGTGCTGCATTCAGCAAAGCATGAGTATG

upper sequence: LOC_Os01g46980.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G070360_T01 (Zea mays), 3'ss of exon 3
tcaatttaattgatggaattaagtttgaaatgccatctccttgtttgttcactactgttattaacaaaataatcattcatcatattgactgg--aaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAAGACCATCATCATGTGGAATCTGTACTGCATTCAGCAAAGAATGAATATG
 ||||       |      || ||   | ||     ||   ||  || |   | |  |||||  ||||  |   |||   ||  |||  ||   |||| ||||| ||||| || |||||||||||||| ||| | |||||||||||||| ||||| || |||||||||||||| |||||||||||||||||| | || ||||
-caatagggccaaatatgctatgtgccatatcagtactttctgcatgctgcttcccattattgtcaaa-catcaattagacagtttgtttgatcaaattcagGGCTTGCTCCGTTTGAAAGAGCCAGCTGTATTGCTCCGTTGCCGCAAGGAAGATCACCATCATGTGGAATCAGTACTGCATTCAGCAAAGCACGAGTATG
















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|33800263|gb|CF325997.1|CF325997
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|33657535|gb|CF280149.1|CF280149
EST:     ATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: ATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|7273928|gb|AU083472.1|AU083472
EST:     GCCACAACCACCATGAATCCAAGACCCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTC-GGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGA
EST: gi|7273929|gb|AU083473.1|AU083473
EST:     GCCACAACCACCATGAATNCAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|40486588|gb|BX898040.1|BX898040
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|1632714|gb|C20443.1|C20443
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|56550159|gb|CX056263.1|CX056263
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|14981446|gb|BI306124.1|BI306124
EST:     ACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: ACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|58593493|gb|CF991801.1|CF991801
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|29639860|gb|CB644869.1|CB644869
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|218488190|gb|FG970074.1|FG970074
EST:     GCCACAACCACCATGAATATAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|58586214|gb|CF984522.1|CF984522
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|55411972|gb|CV724348.1|CV724348
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|33657103|gb|CF279717.1|CF279717
EST:     TTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCCGTTGCCGCAAAGA
genomic: TTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCT-CCGTTGCCGCAAAGA
EST: gi|7273805|gb|AU083349.1|AU083349
EST:     CCACAAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: CCAC-AACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|33800740|gb|CF326240.1|CF326240
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|86251532|gb|CI016821.1|CI016821
EST:     TGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: TGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|88392356|gb|CI612830.1|CI612830
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGC
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGC
EST: gi|33691600|gb|CF319839.1|CF319839
EST:     ATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTNCCGTTGCCGCAAAGA
genomic: ATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCT-CCGTTGCCGCAAAGA
EST: gi|33794426|gb|CF323097.1|CF323097
EST:     TGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: TGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
EST: gi|33688006|gb|CF316245.1|CF316245
EST:     GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAG                         GGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA
genomic: GCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAA

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: 74 (upstream exon), 73 (downstream exon)
Score: 154

TTTGGTTAATTCCATGAAAGAGGATGCTACAAAGCAACTCCTGCGTGTCAGCCACAACCACCATGAATACAAGAACCTTTTGAAAGAACTCGTCGTTCAGgtttgtatga ... ggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAAGACCATCATCATGTGGAATCTGTACTGCATTCAGCAAAGAATGAATATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcactactgttattaacaaaataatcattcatcatattgactggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAAGACCATCATCATGTGGAATCTGTACTGCATTCAGCAAAGAATGAATATG
            ttattaacaaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatttaattgatggaattaagtttgaaatgccatctccttgtttgttcactactgttattaacaaaataatcattcatcatattgactggaaatacagGGTTTGCTTCGGTTGAAAGAGCCAGCGGTACTTCTCCGTTGCCGCAAAGAAGACCATCATCATGTGGAATCTGTACTGCATTCAGCAAAGAATGAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - -ttgatgg
- - - - - - - - - - - - - - - tgccatc
- - - - - - - - - - - - - - - - - - - - - - - - - actactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattcat