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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagctgtaaaaatgctaagtgatagttctaactgaggctccaagttttgaagaaaaagactacagtttggttagttaaccatgtttactgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG

Basic information

species Oryza sativa
transcript LOC_Os08g07960.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 10
------ttgagctgtaaaaatgctaagtgatagttctaactgaggctccaagttttgaagaaaaagactacagtttggttagttaaccatgtttactgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG
      | | ||||||| || | |     ||  |  ||||||    ||| ||  |  |   |     ||    |     |  ||||||||   | |||  ||  |||| ||||||||||||||||||||||| ||||| |||||||||||  |||||||||||||||||||||| ||||||||||||
tgttgttagtgctgtaacaa-gtttttgaattttgataactgcccatcctagcgtctacctatc---cttttatcca--tgtttaaccatcactgctggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG
















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|29681301|gb|CB677576.1|CB677576
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86496217|gb|CI138850.1|CI138850
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86494783|gb|CI137416.1|CI137416
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|33805337|gb|CF328546.1|CF328546
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|66920288|gb|CX107136.1|CX107136
EST:     ATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: ATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86498360|gb|CI140993.1|CI140993
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86597807|gb|CI276593.1|CI276593
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86421137|gb|CI057126.1|CI057126
EST:     GTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: GTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86503924|gb|CI146557.1|CI146557
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|88243189|gb|CI244311.1|CI244311
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86494924|gb|CI137557.1|CI137557
EST:     ATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: ATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86498473|gb|CI141106.1|CI141106
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGT-GGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86495339|gb|CI137972.1|CI137972
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86504575|gb|CI147208.1|CI147208
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86489810|gb|CI132443.1|CI132443
EST:     CTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|87007439|gb|CI279110.1|CI279110
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86428049|gb|CI073146.1|CI073146
EST:     ATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: ATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|89198870|gb|CI003607.1|CI003607
EST:     CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
EST: gi|86494277|gb|CI136910.1|CI136910
EST:     CTATTCCTTGCAGTACCTTCAACAATGATGGGTCGATATTTGCTTATGCA                         GTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA
genomic: CTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCA

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: 69 (upstream exon), 67 (downstream exon)
Score: 35

GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtcaag ... tgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgaagaaaaagactacagtttggttagttaaccatgtttactgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG
                             agttaac  putative branch site (score: 35)
      aagaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagctgtaaaaatgctaagtgatagttctaactgaggctccaagttttgaagaaaaagactacagtttggttagttaaccatgtttactgttaaccagGTCTGCTATGACTGGAGCCGTGGGGCTGAAAACCACAACCCTGCCACTGCAAAGACATCCATCTATCTTCACAGTCCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- -agctgta
- - - - - - -atgctaa
- - - - - - - - - - - - - - - - -ctgaggc
- - - - - - - - - - - - - - - - - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttt