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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggaactataagtctatcacccttgtctggaactatcattctgttatatgtgcccgtctttctctcatcttgcttcaacaggttatccttctgtaccctttagatactgatgcaccttttatccttttctcttttatcacgtcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGGATAGAGAAGGAGCTTGCTGAATTGCAGGAGATGAAG

Basic information

species Oryza sativa
transcript LOC_Os08g37320.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g37320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G157018_T01 (Zea mays), 3'ss of exon 3
--------------------------------------gtgaggaactataagtctatcacccttgtctggaactatcattctgttata-tgtgcccgtctttctctcatct-tgc-ttcaacaggtta---tccttctgtacccttta----gatactgatgcaccttttatccttttctcttttatcacgtcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGGATAGAGAAGGAGCTTGCTGAATTGCAGGAGATGAAG
                                       | |    ||  || |||||  |  || | ||    |   ||  ||   |  | | ||    ||||    ||   ||| | |||    |||    || | |  || | |||      | ||||||  | | || |   ||  | | ||   | || |  || || ||| |||  | || || || || || |||  || |||||||||||| |||||||||||||| ||||||||| || |||| |||| |
gtcagcagctgttgctctcacacttttgtattttaaagtttattgcctgaaaatctatt-ctgttttttgtgttttctatcttgagttgctctaccaacatttcctagatgagtgcatccaattttttagttcccgtattaactccttaccttattgctgatgtgcttctttttggttcttatatt--tatgttacctgtagATTGCTGAATTAAAGGAGGCTGAGAAAGAGCATCAGAAGGAGTCAGAAAGGATAGAGAAGGAACTTGCTGAAATGGAGGAAATGAGG
















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|33682142|gb|CF310381.1|CF310381
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|88238980|gb|CI240142.1|CI240142
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|32948236|gb|BP184808.1|BP184808
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|33680057|gb|CF308296.1|CF308296
EST:     GTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: GTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|163925925|gb|EG714977.1|EG714977
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|33803307|gb|CF327527.1|CF327527
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|58669670|gb|CK058356.1|CK058356
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|163926597|gb|EG713613.1|EG713613
EST:     GTACCGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: GTA-CGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|29676939|gb|CB673214.1|CB673214
EST:     GTACAAGCCAAAGTTTGACGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: GTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|33802541|gb|CF327143.1|CF327143
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|58030598|gb|CX728141.1|CX728141
EST:     CAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: CAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|163920020|gb|EG709826.1|EG709826
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|33661510|gb|CF292477.1|CF292477
EST:     GTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: GTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|33683470|gb|CF311709.1|CF311709
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|5456492|gb|AU075803.1|AU075803
EST:     GTACCGTTGACCCCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGANGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: GTA-CGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|33662295|gb|CF293262.1|CF293262
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTTTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|163918517|gb|EG711627.1|EG711627
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGC
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGC
EST: gi|32947994|gb|BP184566.1|BP184566
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|163920610|gb|EG711789.1|EG711789
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCATAGCTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|27577854|gb|CB000549.1|CB000549
EST:     AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: AGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
EST: gi|33679750|gb|CF307989.1|CF307989
EST:     CAGTACAAGCCAAAGTTTGATGCGCTG                         CTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG
genomic: CAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGG

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: 66 (upstream exon), 75 (downstream exon)
Score: 174

GCATTGAAATCCCCAAGTACGTTGACACCGTGACTCCTCAGTACAAGCCAAAGTTTGATGCGCTGgtgaggaact ... tcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGGATAGAGAAGGAGCTTGCTGAATTGCAGGAGATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttagatactgatgcaccttttatccttttctcttttatcacgtcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGGATAGAGAAGGAGCTTGCTGAATTGCAGGAGATGAAG
        tactgat  putative branch site (score: 174)
                  ccttttatccttttct  putative PPT
                                 tcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggaactataagtctatcacccttgtctggaactatcattctgttatatgtgcccgtctttctctcatcttgcttcaacaggttatccttctgtaccctttagatactgatgcaccttttatccttttctcttttatcacgtcatatgcagCTTGTTGAGCTGAAAGAAGCAGAAAAGGAGTCTCTGAAGGAGTCAGAGAGGATAGAGAAGGAGCTTGCTGAATTGCAGGAGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG