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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaacttggaatttctgccttctgcaccatgaacttgtctctctggtgtcactctaagcaatattttgacatgggttgctttgcgtgtttgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTTGAGGATGAGGGGAACCGTGAGCACCTGGAGGTTGCCTGCGACCTTGCAA

Basic information

species Oryza sativa
transcript LOC_Os01g06460.1
intron # 2
splice site 3'
intron type U2

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|88661729|gb|CI458891.1|CI458891
EST:     ACGATACAATCTTGA-                         GGTAGCCTTGAGGCTTTCACTAAGCAATTTGGGTGCTGCC-TGGCCCTTGT
genomic: ACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGG-CCTTGT
EST: gi|86592516|gb|CI253197.1|CI253197
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88841887|gb|CI081143.1|CI081143
EST:     CGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: CGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|89187780|gb|CI009764.1|CI009764
EST:     TCTCATCACACTCGTACAGCTATTCGTCGACGATACCATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: TCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|86508358|gb|CI150991.1|CI150991
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88201714|gb|CI202069.1|CI202069
EST:     GGTTCGCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTGTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88201698|gb|CI202053.1|CI202053
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88210030|gb|CI209879.1|CI209879
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88963974|gb|CI032891.1|CI032891
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|87032586|gb|CI266226.1|CI266226
EST:     TTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: TTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88203772|gb|CI203621.1|CI203621
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|86509888|gb|CI152521.1|CI152521
EST:     CGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: CGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|86419230|gb|CI054031.1|CI054031
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88210159|gb|CI210008.1|CI210008
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88662754|gb|CI473742.1|CI473742
EST:     TATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: TATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88486577|gb|CI423848.1|CI423848
EST:     ACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: ACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88663181|gb|CI478893.1|CI478893
EST:     CTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: CTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|86250965|gb|CI013975.1|CI013975
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88213737|gb|CI213586.1|CI213586
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|86530888|gb|CI171094.1|CI171094
EST:     GTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88832539|gb|CI008135.1|CI008135
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|86823334|gb|CI256332.1|CI256332
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|86527125|gb|CI167331.1|CI167331
EST:     CACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: CACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|86592588|gb|CI253269.1|CI253269
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88661519|gb|CI456043.1|CI456043
EST:     TACAGCTATTCNTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTNCCATGGCCTTGTT
genomic: TACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88231650|gb|CI231499.1|CI231499
EST:     CACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: CACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88207218|gb|CI207067.1|CI207067
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|94363041|gb|CI053202.1|CI053202
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|88209786|gb|CI209635.1|CI209635
EST:     GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
genomic: GGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT
EST: gi|86842870|gb|CI342135.1|CI342135
EST:     TCTCTCA-CACACTCG-ACAGCTATTGGTCGACGATACAATCTTGAG                         GGTAGCTTTGAGGCTTTCACTAAACAATGTGGGGGCTGCCATGGCCTTGTT
genomic: TCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTT

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: 64 (upstream exon), 72 (downstream exon)
Score: 52

CCTCTATATGCTTGGGAATGCTCTCTTCGGGTGGAACTGCATAGCCCCATGGTTCTCTCATCACACTCGTACAGCTATTCGTCGACGATACAATCTTGAGgcaagttttg ... tgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTTGAGGATGAGGGGAACCGTGAGCACCTGGAGGTTGCCTGCGACCTTGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgtcactctaagcaatattttgacatgggttgctttgcgtgtttgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTTGAGGATGAGGGGAACCGTGAGCACCTGGAGGTTGCCTGCGACCTTGCAA
                   ttttgac  putative branch site (score: 52)
                                           tttgtctttc  putative PPT
               aatattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaacttggaatttctgccttctgcaccatgaacttgtctctctggtgtcactctaagcaatattttgacatgggttgctttgcgtgtttgtctttcagGGTAGCTTTGAGGCTTTCACTAAGCAATGTGGGTGCTGCCATGGCCTTGTTGAGGATGAGGGGAACCGTGAGCACCTGGAGGTTGCCTGCGACCTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - -ttctgcc
- - - - - - - - - - ttctgca
- - - - - - - - - - - - - - catgaac
- - - - - - - - - - - - - - - - - - - - - tctggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcgtgt