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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtactactactcttttcatttccatgtttgagctctgttgtgccattgatgatcaccacatttaatttgcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG

Basic information

species Oryza sativa
transcript LOC_Os01g36930.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 14
--gtagtactactactcttttcatttccatgtt-tgagctctgttgtgccattgatgatcacc-acatttaatttgcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG
  |   |     | | || |||| ||    |||   | |    ||||  ||||  ||||     |   | ||||||||||| |||||||||||||||||||||||||| ||| |||||||    | ||| || || || |||||||||||||||||||||
gtgctttctcttttcactattcagttttgagttgccaacatcattgttgcattattgattttggatgctcaatttgcatgtaaagATGCTGAGAGATGCAGAAAATGCAAAGCTTGGATT----GTACATGGGAAAGCTAGCAGCTCAAAAGAAAATGAG

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 13
---gtagtactactactcttttcatttccatgtt-tgagctctgttgtgccattgatgatcacc-acatttaatttgcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG
   |   |     | | || |||| ||    ||| | | |  | |||| ||| |  ||||     |   | |||||||| || |||||||||||||||||||||||||| ||||||||||| ||||||||||| || || ||| |||  ||||||||||||
gtagctttctcttttcactattcagttttgagttgtcaacattattgttccagtattgattttggatgctcaatttgcacgtaaagATGCTGAGAGATGCAGAAAATGCAAAGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG
















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|163920010|gb|EG709816.1|EG709816
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|33803665|gb|CF327708.1|CF327708
EST:     CAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: CAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|86251819|gb|CI019011.1|CI019011
EST:     ACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|29615419|gb|CB620431.1|CB620431
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|29646292|gb|CB651299.1|CB651299
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|29674106|gb|CB670381.1|CB670381
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|29679501|gb|CB675776.1|CB675776
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|58686515|gb|CK075202.1|CK075202
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|29667425|gb|CB663700.1|CB663700
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|66916241|gb|CX103089.1|CX103089
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|58676643|gb|CK065330.1|CK065330
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|29615344|gb|CB620356.1|CB620356
EST:     ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
EST: gi|29689096|gb|CB685371.1|CB685371
EST:     ATGACTNTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAG                         ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG
genomic: ATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAG

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: 65 (upstream exon), 60 (downstream exon)
Score: 27

AAAGTTGATTACCCGCTGGAACTGGATGTTTATGACTTTTGCTCAGATGAACTGAAACAAAAACTCCAAGCTCCCCGACAGgtagtactac ... gcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttgagctctgttgtgccattgatgatcaccacatttaatttgcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG
                                    atttaat  putative branch site (score: 27)
                                  acatttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtactactactcttttcatttccatgtttgagctctgttgtgccattgatgatcaccacatttaatttgcatgtgaagATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA