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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGTGGTTCTGCATGAGGGGGATGCCAAAGATTGGGTTTACAAAGGAGAAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcgaataggttctgcttgtgtcattattggttactgacctatagtctcccgtaaatcggcgaatttgatgcatgtgcttcaagaaggatgttt...

Basic information

species Oryza sativa
transcript LOC_Os04g56580.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56580.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G067299_T02 (Zea mays), 5'ss of exon 2
GGAGGTGGTTCTGCATGAGGGGGATGCCAAAGATTGGGTTTACAAAGGAGAAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcgaataggttctgcttgtgtcattattggttactgacctatagtctcccgtaaatcggcgaatttgatgcatgtgcttcaagaaggatgttt-----
||| | ||||||||| |  | ||||||||| |||||||||||||| || ||||| || |||||||| |||||||||||||| |||||||| || || |||||| ||   || ||||||||   || ||    |      |  || |  | |  |   |    ||   |  | |||| || | |   |   |     | |      
GGATGGGGTTCTGCAAGCCGCGGATGCCAAGGATTGGGTTTACAAGGGGGAAGGCGCCGCGAATCTTATCCTCAGCTACACCGGCTCGTCGCCCTCCATGgtaagcgctgagtaggttcttactgagtgtgcac---gcatcgatcacttgattttaggggctcaatg--tgtgattcacgggtgccgccattcgagctccagat

upper sequence: LOC_Os04g56580.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G150496_T01 (Zea mays), 5'ss of exon 3
GGAGGTGGTTCTGCATGAGGGGGATGCCAAAGATTGGGTTTACAAAGGAGAAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcgaataggttctgcttgtgtcattattggttactgacctatagtctcccgtaaatcggcgaatttgatgcatgtgc---ttcaagaaggatgttt
| | | ||||||||| |  | |||||||||  | ||||||||||| || || || || |||||||| |||||||||||||| ||||| || ||| |||||||||||   || ||| |||   || | | |||||   |   |  |    ||| |   |    |  | |   || | |  ||||    ||| ||    |  |  
GAATGGGGTTCTGCAAGCCGCGGATGCCAAGTACTGGGTTTACAAGGGTGAGGGCGCCGCGAATCTCATCCTCAGCTACACCGGCTCATCCCCTACTATGgtatgcgctgagtagattcctatt-tcttattatgcctgcatcgcagcgagtttaggggctctatgtgtgattcacgggtgtggccattccagccccagat--
















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|88352153|gb|CI613804.1|CI613804
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88741376|gb|CI764884.1|CI764884
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88328891|gb|CI646968.1|CI646968
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88460113|gb|CI695314.1|CI695314
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88367935|gb|CI572656.1|CI572656
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88365048|gb|CI616467.1|CI616467
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|300215843|gb|HO088469.1|HO088469
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88592176|gb|CI710260.1|CI710260
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88378393|gb|CI636340.1|CI636340
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88761945|gb|CI771501.1|CI771501
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88399280|gb|CI618470.1|CI618470
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88334290|gb|CI642535.1|CI642535
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88431424|gb|CI576954.1|CI576954
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88361823|gb|CI681985.1|CI681985
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|95100741|gb|CI692452.1|CI692452
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88336647|gb|CI643972.1|CI643972
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
EST: gi|88390323|gb|CI605776.1|CI605776
EST:     AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATG                         CTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG
genomic: AAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCG

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: 57 (upstream exon), 75 (downstream exon)
Score: 49

GGAGGTGGTTCTGCATGAGGGGGATGCCAAAGATTGGGTTTACAAAGGAGAAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcg ... tcttgaacagCTTGGCAAGGTTCTGCGAGTCAAAAAGATTCTAAAAGACAAGGGACAACCGGCACCAAACTGTATAGTCTTCTCAAGTCATGAGGAACATCTGTGGGGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGTGGTTCTGCATGAGGGGGATGCCAAAGATTGGGTTTACAAAGGAGAAGGTGCAGCGAATCTAATCCTCAGCTACACTGGCTCGTCACCTTCTATGgtatgcatcgaataggttctgcttgtgtcattattggttactgacctatagtctcccgtaaatcggcgaatttgatgcatgtgcttcaagaaggatgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT