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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcaatcccatctgaaaattcgaactcaccatgacattctatgttttatttccttttagttattgcttgtactttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTGCCCGAGGAGGAGCTCCTGACCTCAACACTAGCTGCAAAGTTGAATGCAT

Basic information

species Oryza sativa
transcript LOC_Os06g04650.1
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|313080053|gb|HO213373.1|HO213373
EST:     CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGA
genomic: CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGA
EST: gi|3760326|gb|C97580.1|C97580
EST:     CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
EST: gi|58588478|gb|CF986786.1|CF986786
EST:     CAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
EST: gi|58670851|gb|CK059537.1|CK059537
EST:     CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
EST: gi|10930950|gb|AU161224.1|AU161224
EST:     CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
EST: gi|89167247|gb|CI252778.1|CI252778
EST:     CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
EST: gi|27577735|gb|CB000430.1|CB000430
EST:     CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
EST: gi|38470045|gb|CF954176.1|CF954176
EST:     CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
EST: gi|87024018|gb|CI252765.1|CI252765
EST:     CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
EST: gi|58031306|gb|CX728849.1|CX728849
EST:     CAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
EST: gi|9788933|gb|BE530943.1|BE530943
EST:     CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAG                         AAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG
genomic: CACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTG

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), 69 (downstream exon)
Score: 20

TCTTAGCAAAGAAAAAGAACAAGCTAAGGATCGCCGCAGTGTCATTACCACACAGATCCAACCAATAGGTGCATTTTATCCGGCTGAACCGGAACATCAGgtagcaatcc ... actttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTGCCCGAGGAGGAGCTCCTGACCTCAACACTAGCTGCAAAGTTGAATGCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaccatgacattctatgttttatttccttttagttattgcttgtactttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTGCCCGAGGAGGAGCTCCTGACCTCAACACTAGCTGCAAAGTTGAATGCAT
 aactcac  putative branch site (score: 20)
                  ttttatttccttttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcaatcccatctgaaaattcgaactcaccatgacattctatgttttatttccttttagttattgcttgtactttggtagAAATTTGAGCTGAAGCGCAAGCCGTTTCTCCTGCAACTGATTGGGAACCTGCCCGAGGAGGAGCTCCTGACCTCAACACTAGCTGCAAAGTTGAATGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG