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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttgaaagacgaaacattgagagggaaaacaaggaactcctgtattctgattctgatttagcaggaccatgatgcattttcttttgttttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCTAAACAAGCTATGCGAAGCCTTGTCACTCCTTTACGTATGAACGAGGGAA

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 1
atcttgaaag-acgaaacattgagagggaaaacaaggaactcctgtattctgattctgat-ttagcaggaccatgatgcattttcttttgttttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCTAAACAAGCTATGCGAAGCCTTGTCACTCCTTTACGTATGAACGAGGGAA
 | || ||   | |||  | | |   |     |||   | |     | | | ||    || |  | || ||     ||  | || ||| || | || ||||||||||||||||| |||||||||| |||||||||||||| ||||| ||||| |||||||||||||| ||||||||||| || ||||| ||||| | ||| |
gttttaaactcaagaagtactcatgagcgcttcaac--attttatcactttaataaccatgtccgaagcactgacgtgtgtcttatttcgtgtccactatagGTCTGCAGTAAGCTTTGTGAAAAGTTTGGAAAGCATGGTCTGGTGAAACCGAAACAAGCTATGCGCAGCCTTGTCACACCATTACGAATGAATGCGGGGA

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 1
atcttgaaagacgaaacattgagagggaaaacaaggaactcctgtattctgattctga----tttagcaggaccatgatgcattttctttt------gttttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCTAAACAAGCTATGCGAAGCCTTGTCACTCCTTTACGTATGAACGAGGGAA
          ||  ||  |  |     |  |||     |   |||||||   |  |||    |||       || | ||| || || || |      |  || |    |||| ||||| |   | |||||||||||||||||||||||  |||| || || ||||  ||| ||||||||||||   | || ||  | |||   || ||||
----------acagaatttaaatgtttactacagttctcatgtgtattccattaatgaagttttttctttttccttcatgaatcttattgtcaatgagactttatggcagGTTTGCAGCATACTATGTGAAAAATTTGGAAAGCATGGATTGGTTAAGCCAAAACCTGCTGTGCGAAGCCTTGCAGCGCCCTTGAGAATGTTTGATGGAA
















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|29623430|gb|CB628441.1|CB628441
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88575412|gb|CI669557.1|CI669557
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88420855|gb|CI620173.1|CI620173
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88359491|gb|CI621022.1|CI621022
EST:     ACCTCCTCATCGAGGCTCGGTGCGTAGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88594152|gb|CI711391.1|CI711391
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCCAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88423363|gb|CI576488.1|CI576488
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88717626|gb|CI741136.1|CI741136
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGANGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88731053|gb|CI754666.1|CI754666
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88347463|gb|CI637403.1|CI637403
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGCTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88724350|gb|CI747609.1|CI747609
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88763977|gb|CI773393.1|CI773393
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88585189|gb|CI702802.1|CI702802
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88721214|gb|CI744513.1|CI744513
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88442851|gb|CI694255.1|CI694255
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|66915780|gb|CX102628.1|CX102628
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88582946|gb|CI699414.1|CI699414
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|29627492|gb|CB632503.1|CB632503
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|117239285|gb|CT849366.1|CT849366
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88587455|gb|CI705201.1|CI705201
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88695738|gb|CI737776.1|CI737776
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88765367|gb|CI774461.1|CI774461
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
EST: gi|88305044|gb|CI626714.1|CI626714
EST:     ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAG                         GTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT
genomic: ACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCT

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: 58 (upstream exon), 63 (downstream exon)
Score: 64

CTTCGACTTCGGCGCCCCCGACGGCCACGGCATCTTCGACGCGCTCGGCGACCTCCTCATCGACGCTCGGTGCGTCGCCGACGAGGAGCACTGCCTCGAGgtaccacgcg ... ttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCTAAACAAGCTATGCGAAGCCTTGTCACTCCTTTACGTATGAACGAGGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctgattctgatttagcaggaccatgatgcattttcttttgttttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCTAAACAAGCTATGCGAAGCCTTGTCACTCCTTTACGTATGAACGAGGGAA
       ttctgat  putative branch site (score: 64)
                               cattttcttttgtttt  putative PPT
                                attttcttttgttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcttgaaagacgaaacattgagagggaaaacaaggaactcctgtattctgattctgatttagcaggaccatgatgcattttcttttgttttcaatatagGTCTGCAGTAAGATTTGTGAAAAATTTGGAAAGCATGGCCTGGTAAAACCTAAACAAGCTATGCGAAGCCTTGTCACTCCTTTACGTATGAACGAGGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT