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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctttcaaagcaagagtcacactttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG

Basic information

species Oryza sativa
transcript LOC_Os02g40830.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094614_T02 (Zea mays), 3'ss of exon 4
----tatctttcaaagcaagagtcacac-tttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG----------------------
      | | | ||||  |    | ||   ||||| |   | || ||||    || |||   ||| |||   |   | | |    ||  || |    || |  |||||||||| ||||||||||| || |||   |||||||||||||| |||||||||||||| ||||| ||||||||||||                      
ctatgctgtatgaaagtcattacctcatgcttttagtttgcaatatttccttgcatatc---gaagatttctagagattgatactgt--atgttctcttcggtagGTCTACTTGTGTGAGAAACTATCTCTTACAAATGAGATGTACTTTGCCATCACCCTTGATAGGAAAACTGCTGGTCCGGTATGCCATTTATCTCAAATAT

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094614_T01 (Zea mays), 3'ss of exon 4
----tatctttcaaagcaagagtcacac-tttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
      | | | ||||  |    | ||   ||||| |   | || ||||    || |||   ||| |||   |   | | |    ||  || |    || |  |||||||||| ||||||||||| || |||   |||||||||||||| |||||||||||||| ||||| ||||||||||||
ctatgctgtatgaaagtcattacctcatgcttttagtttgcaatatttccttgcatatc---gaagatttctagagattgatactgt--atgttctcttcggtagGTCTACTTGTGTGAGAAACTATCTCTTACAAATGAGATGTACTTTGCCATCACCCTTGATAGGAAAACTGCTGGTCCG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G064695_T03 (Zea mays), 3'ss of exon 4
----tatctttcaaagcaagagtcacac-tttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
      | | | ||||  |    | ||   ||||| |   | || ||||    ||    | |||| |||   |   | | |  |  |  || |    || | ||||||||||| ||||||||||| || |||  |||||||||||||||||||||||||||||| ||||| ||||||||||||
ctatgctgtatgaaagtcattacctcatgcttttagtttgcaatatttccttgca---tattgaagatttctagagattga--tactctatgttctcttcggcagGTCTACTTGTGTGAGAAACTATCTCTTACTAATGAGATGTACTTCGCCATCACCCTTGATAGGAAAACTGCTGGTCCG

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 4
tatctttcaaagcaagagtcacactttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtg---ttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
|     |  |        |    || ||| |  |  | | | |      | | |||  |||   ||    |  |  ||  ||||| || |    |||| |||||| ||||| ||||| || ||||||||||| |||||||||||||| || || || || ||  | |  | ||||||||| 
tgctactttattttgtttttggtctctttcaatccttttatatagagatata-cacaaaaaggggttggttgtttgat--gttgaattttccattttttacagGTTTACTTGTGTGAAAAGCTGTCACTTGTAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCA

upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 4
tatctttcaaagcaagagtcacacttt-ttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtac-----taaattcgttg-atttgtgttttga-cagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
                 || |    || || ||| |   ||||| | ||   || | ||  | |  ||  | ||     |  |||| |||  | |   |||||| ||||| ||||| ||||||||| ||||||| || ||||||||||||||  |||| |  || ||| | ||  ||||||| |||
-------------gtttgttatctgttattcatgattggtgttttttcttctattattgtcactgctcttgcacctttgtttattcattgtgtcttcattttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG

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|163928461|gb|EG715441.1|EG715441
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|66913068|gb|CX099916.1|CX099916
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|58681651|gb|CK070338.1|CK070338
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTG
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTG
EST: gi|88361440|gb|CI605221.1|CI605221
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|55434355|gb|CV730299.1|CV730299
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTG
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTG
EST: gi|58668786|gb|CK057472.1|CK057472
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTC
EST: gi|29662328|gb|CB658603.1|CB658603
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|58588874|gb|CF987182.1|CF987182
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|4714828|gb|AU055945.1|AU055945
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|29662110|gb|CB658385.1|CB658385
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|38478366|gb|CF962499.1|CF962499
EST:     AGATTCTGGTAACAAAAGAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|58684186|gb|CK072873.1|CK072873
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|58588447|gb|CF986755.1|CF986755
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAAATGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|33688588|gb|CF316827.1|CF316827
EST:     GATTCTGGTAACAAAACAAACTGGTCCACAGGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: GATTCTGGTAACAAAACAAACTGGTCCACAGGGG-AAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|88730444|gb|CI754057.1|CI754057
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|4880970|gb|AU065269.1|AU065269
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GGTCTAATTTATGTGAGGAAACTGTCANTTGTTAATG
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagG-TCTACTT-ATGTGAG-AAACTGTCACTTGTTAATG
EST: gi|58592643|gb|CF990951.1|CF990951
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|33794775|gb|CF323267.1|CF323267
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
EST: gi|27577186|gb|CA999880.1|CA999880
EST:     AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG                         GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC

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: 65 (upstream exon), 73 (downstream exon)
Score: 82

CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
                         tactaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatctttcaaagcaagagtcacactttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - aaagcaa
- - - - - - - - - - - - - - -aatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgatt