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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttgaaacaggctcttgagtttatgtttgtcctttattttactttatgctgaaattatgtcctacaactcttctgttcatgttttacatagtagatgcctagatcgtcatcgtcgtgaaattttcggaatgacaaacccttttgacattttccttatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGTCCCATCTGCAGGCAACCTGTGGAGCGTTTGCTCGAGATCAAAGTCAACA

Basic information

species Oryza sativa
transcript LOC_Os10g13670.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g13670.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G09770.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagtcttgaaacaggctcttgagtttatgtttgtcctttattttactttatgctgaaattatgtcctacaactcttctgttcatgttttacatagtagatgcctagatcgtcatcgtcgtgaaattttcggaatgacaaacccttttgacattttccttatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGTCCCATCTGCAGGCAACCTGTGGAGCGTTTGCTCGAGATCAAAGTCAACA
                                                                             |  ||  | | |    ||  |  |   |||    || ||  | |  | || |   || ||  |||   | ||    ||    |  |||||||||||||||| ||||  || || |||||  ||||||  ||||| || ||||| ||||| |||||||||||||| ||  |  |  | ||||| |||||  || 
----------------------------------------------------------------------------gtaagtgaaagct---gatgatttactactattatgtgatgatggacatatatataga-tgttaaaaattgtttgggtt----tggtggtgcagTGTATGTGTAGCGGATGTGCTAAGGTATTGAGGTTTCAGACAAATCGATGCCCCATTTGCAGGCAACCTGTTGAAAGGCTTTTGGAGATAAAAGTTCACG

upper sequence: LOC_Os10g13670.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ16057 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtcttgaaacaggctcttgagtttatgtttgtcctttattttactttatgctgaaattatgtcctacaactcttctgttcatgttttacatagtagatgcctagatcgtcatcgtcgtgaaattttcggaatgacaaacccttttgacattttccttatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGTCCCATCTGCAGGCAACCTGTGGAGCGTTTGCTCGAGATCAAAGTCAACA
                                                                                                           | | |  ||   | |    |||||   ||  |      ||||    ||||  |  |  ||||||||||||| ||||||||||| || || ||||||| |||||| ||||| || || || || |||   |||||||||||  ||||||||||||| ||    |
-------------------------------------------------------------------------------------------------------gtaggctggctatatacttctggttttc---atagctctttttttttttttttttttcttcttgcagTGTATGTGTAGCGAGTGCGCCAAAGTGCTGAGGTTCCAGACGAACCGCTGCCCGATTTGTAGGTGCCCTGTGGAGCGACTGCTCGAGATCAAGGTTCCAA

upper sequence: LOC_Os10g13670.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ16938 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtcttgaaacaggctcttgagtttatgtttgtcctttattttactttatgctgaaattatgtcctacaactcttctgttcatgttttacatagtagatgcctagatcgtcatcgtcgtgaaattttcggaatgacaaacccttttgacattttccttatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGTCCCATCTGCAGGCAACCTGTGGAGCGTTTGCTCGAGATCAAAGTCAACA
                                                                                     |    |   || || ||  || | |  ||||||     |  ||||     |      | || |     | |  ||  |  ||||||||||||| ||||||||||| || || ||||||| |||||| ||||| || || || || |||   || ||||||||  ||||||||||||| ||    |
------------------------------------------------------------------------------------gtaggctggcta-tatatttct-ggttttcatcgctcatagttttttttttt------ctctctctctctctctctcgtt-tgcagTGTATGTGTAGCGAGTGCGCCAAAGTGCTGAGGTTCCAGACGAACCGCTGCCCGATTTGTAGGTGCCCGGTGGAGCGACTGCTCGAGATCAAGGTTCCGA

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|88247729|gb|CI247578.1|CI247578
EST:     AACTGTCCTCCCATGTAGACATATG                         TGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT
genomic: AACTGTCCTCCCATGTAGACATATGgtaagtcttg ... tatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT
EST: gi|29660289|gb|CB656564.1|CB656564
EST:     TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATG                         TGTATGTGCAGCGAGTGCGCAAAGGTTCTGAAGTAC
genomic: TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATGgtaagtcttg ... tatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTAC
EST: gi|89198695|gb|CI003432.1|CI003432
EST:     ATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATG                         TGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT
genomic: ATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATGgtaagtcttg ... tatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT
EST: gi|86518027|gb|CI158233.1|CI158233
EST:     TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATG                         TGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT
genomic: TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATGgtaagtcttg ... tatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT
EST: gi|86593939|gb|CI260168.1|CI260168
EST:     TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATG                         TGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT
genomic: TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATGgtaagtcttg ... tatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT
EST: gi|87030163|gb|CI111859.1|CI111859
EST:     TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATG                         TGTATGTGCAGCGAGTGCGCAAAGGTTTTGAGGTTACCAGACCAACCGATG
genomic: TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATGgtaagtcttg ... tatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGG-TACCAGACCAACCGATG
EST: gi|88956644|gb|CI092836.1|CI092836
EST:     TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATG                         TGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT
genomic: TCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATGgtaagtcttg ... tatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGT

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: 73 (upstream exon), 75 (downstream exon)
Score: 16

CTCTGTTGAAGGTGACACCGAAGGGAATGATCCTGGCAAAGAGTGTGTTATCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATGgtaagtcttg ... tatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGTCCCATCTGCAGGCAACCTGTGGAGCGTTTGCTCGAGATCAAAGTCAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtcgtgaaattttcggaatgacaaacccttttgacattttccttatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGTCCCATCTGCAGGCAACCTGTGGAGCGTTTGCTCGAGATCAAAGTCAACA
                              ttttgac  putative branch site (score: 16)
                                    cattttcctt  CT-rich tract
      tgaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttgaaacaggctcttgagtttatgtttgtcctttattttactttatgctgaaattatgtcctacaactcttctgttcatgttttacatagtagatgcctagatcgtcatcgtcgtgaaattttcggaatgacaaacccttttgacattttccttatggtgcagTGTATGTGCAGCGAGTGCGCAAAGGTTCTGAGGTACCAGACCAACCGATGTCCCATCTGCAGGCAACCTGTGGAGCGTTTGCTCGAGATCAAAGTCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA