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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacttgcctgcaattatatgaaaccaataggatcagatatcgctatattcatgcttgtgaaacaagaaatggtcttattgttttgactttttccaaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g37910.1
intron # 3
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|58610712|gb|CK038424.1|CK038424
EST:     CGATCATATTTTCATTTTTTACAGTGACCAGGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|33799061|gb|CF325390.1|CF325390
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|58688754|gb|CK077441.1|CK077441
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|58607687|gb|CK035720.1|CK035720
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|58691139|gb|CK079826.1|CK079826
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|4715544|gb|AU056660.1|AU056660
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|58692937|gb|CK081624.1|CK081624
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|58688098|gb|CK076785.1|CK076785
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|58691202|gb|CK079889.1|CK079889
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|58692544|gb|CK081231.1|CK081231
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|163923567|gb|EG713308.1|EG713308
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|58690742|gb|CK079429.1|CK079429
EST:     CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: CGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
EST: gi|58591094|gb|CF989402.1|CF989402
EST:     GGGGGTCCTGGTGTCCTTG                         GGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA
genomic: GGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGA

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: 75 (upstream exon), 73 (downstream exon)
Score: 109

AAAACTGCTGTCAAAGGTGGGAGTGGCAAAGTCCTGGACAGTGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTGgtgagtactt ... aaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcttgtgaaacaagaaatggtcttattgttttgactttttccaaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG
                               ttttgac  putative branch site (score: 109)
                                     ctttttcca  CT-rich tract
                                      tttttccaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacttgcctgcaattatatgaaaccaataggatcagatatcgctatattcatgcttgtgaaacaagaaatggtcttattgttttgactttttccaaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT