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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcttttttccttgtaacttcctttttcattcacattgttttgtgatcactaagaacagcacaacaaaacataattcggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCACGAGGGTCGCCTACTACAGGAGCTACATCACCAAGCTGAAGGAGGCGAT

Basic information

species Oryza sativa
transcript LOC_Os01g32364.1
intron # 10
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|89174123|gb|CI042016.1|CI042016
EST:     GAAGTATGGTAACCCCACCATGTTTCTATCTGAAAATG                         GCATGGATGATCCTGGCAATGTGACCCTTGCTCAGGGGGTGCATGACACCA
genomic: GAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
EST: gi|218495463|gb|FG950142.1|FG950142
EST:     CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGACAATG                         GCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
genomic: CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
EST: gi|87018970|gb|CI256855.1|CI256855
EST:     CTATGTCAAGGAGAAGTATGGCAACCCCACAATGTTTCTATCTGAAAATG                         GCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
genomic: CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
EST: gi|86841673|gb|CI337369.1|CI337369
EST:     CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCT-AAAATG                         GCATGGATGATCCTGGCAATGTGGCCATTGCTCAGGGGGTGCATGACACCA
genomic: CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
EST: gi|88968373|gb|CI098615.1|CI098615
EST:     CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATG                         GCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
genomic: CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
EST: gi|86493335|gb|CI135968.1|CI135968
EST:     CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATG                         GCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
genomic: CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
EST: gi|88249368|gb|CI249217.1|CI249217
EST:     TATGGTAACCCCACAATGTTTCTATCTGAAAATG                         GCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
genomic: TATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
EST: gi|86259344|gb|CI008021.1|CI008021
EST:     CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATG                         GCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
genomic: CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
EST: gi|86436220|gb|CI117942.1|CI117942
EST:     CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATG                         GCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
genomic: CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
EST: gi|88271678|gb|CI387731.1|CI387731
EST:     ATGTTTCTATCTGGAAATGG                         GCATGGATTATCCTGGCCCATGTGACCCTTGCTCAGGGGGTGCATGACAC
genomic: ATGTTTCTATCTGAAAAT-Ggtacatcttt ... cggttttcagGCATGGATGATCCTGG-CAATGTGACCATTGCTCAGGGGGTGCATGACAC
EST: gi|86879899|gb|CI339981.1|CI339981
EST:     CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATG                         GCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA
genomic: CTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCA

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: 68 (upstream exon), 70 (downstream exon)
Score: 19

AATTCTGACTGGCTTTACATTGTACCGTGGGGTTTGTACAAAGCTGTCACCTATGTCAAGGAGAAGTATGGTAACCCCACAATGTTTCTATCTGAAAATGgtacatcttt ... cggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCACGAGGGTCGCCTACTACAGGAGCTACATCACCAAGCTGAAGGAGGCGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacattgttttgtgatcactaagaacagcacaacaaaacataattcggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCACGAGGGTCGCCTACTACAGGAGCTACATCACCAAGCTGAAGGAGGCGAT
                                                ttttc  CT-rich tract
                               aacaaaacataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatcttttttccttgtaacttcctttttcattcacattgttttgtgatcactaagaacagcacaacaaaacataattcggttttcagGCATGGATGATCCTGGCAATGTGACCATTGCTCAGGGGGTGCATGACACCACGAGGGTCGCCTACTACAGGAGCTACATCACCAAGCTGAAGGAGGCGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG