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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcattctttctgctgcaatggtgttcatcaatatttacatttgtttgacaatatgcatttgcatttattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGGGACAATGGTTACCGGATAACTGCAACTGCTGCAACCTGGGATCAGGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g54100.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G095634_T01 (Zea mays), 3'ss of exon 7
-------------------gtagcattctttctgctgcaatggtgttcatcaatatttaca--tttgtttgacaatatgc-atttgcatttattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGGGACAATGGTTACCGGATAACTGCAACTGCTGCAACCTGGGATCAGGCTG
                     | |  |    |  || |     |  ||  |    |||| |   | ||||   | |   | ||| ||||||| ||| ||||| || |||||||| ||| | || ||||| |||||||||||  | || |||||||  |||||| ||||||| ||| || |||| || || ||||||||||
gagtcgttcagatcgactatcacctctgcaccgacttctcgactagtcgcccgactttaaaacctcgtttcttattgaactattggcatttactttccagGTGGTTGAACTGGATTTCTTGTATCCCAGCGAGGGAATTCATAAAAGGTGGGACAGGGGTTACTGGATAACCGCAGCTCCTGCTACTTGTGATCAGGCTG

upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 14
gtagcattctttctgctgcaatg-gtgttcatcaatatttacatttgtttgacaatatgcatttgcattta---ttttac----agGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGGGACAATGGTTACCGGATAACTGCAACTGCTGCAACCTGGGATCAGGCTG
      || | | |  || |||   | | |||  ||  |     | ||   | |  | |  |||    ||    ||||||    ||||||| || || || ||  | || || ||||| || ||||| | ||| ||||| |||||||| || || || |||||||| ||||||||||| |||||||
--gttcttttgtgttttggaatctatctccattcatgctatttgtggtagcaaagaaggtgtttctgattgattttttacttgtagGTTGTAGAGCTAGATTTTTTGTATCCTAGTGAAGGTATTCATCGGAGGTGGGATAATGGTTATCGCATCACAGCAACTGCAGCAACCTGGGACCAGGCTG
















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|29687708|gb|CB683983.1|CB683983
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|9865453|gb|AU101203.1|AU101203
EST:     AAGTAGATGGGCCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: AAGTAGATGGG-CAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|58692699|gb|CK081386.1|CK081386
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|58693298|gb|CK081985.1|CK081985
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|29687566|gb|CB683841.1|CB683841
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|25806191|gb|CA762152.1|CA762152
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATNTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|218494323|gb|FG952810.1|FG952810
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|86889762|gb|CI299960.1|CI299960
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|29625957|gb|CB630968.1|CB630968
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|163919775|gb|EG710337.1|EG710337
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACC
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACC
EST: gi|58687467|gb|CK076154.1|CK076154
EST:     GTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|58692454|gb|CK081141.1|CK081141
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|58654345|gb|CK043025.1|CK043025
EST:     GAAGTAGATGGTCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|58591468|gb|CF989776.1|CF989776
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCGGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|58692206|gb|CK080893.1|CK080893
EST:     GAAGTAGATGGTCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
EST: gi|38565581|gb|CK085034.1|CK085034
EST:     GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAG                         GTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG
genomic: GAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGG

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: 70 (upstream exon), 52 (downstream exon)
Score: 14

AAACAAGAAATGGAGGGACGGTTTTTATGTGACTTCCATGGCAACAGCTGGAAGTAGATGGGCAGTTGTTATGTCGCGTAATGCTGGATTTTCTGATCAGgtagcattct ... tattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGGGACAATGGTTACCGGATAACTGCAACTGCTGCAACCTGGGATCAGGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttcatcaatatttacatttgtttgacaatatgcatttgcatttattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGGGACAATGGTTACCGGATAACTGCAACTGCTGCAACCTGGGATCAGGCTG
                      gtttgac  putative branch site (score: 14)
                                           tttatttt  putative PPT
         aatatttacatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcattctttctgctgcaatggtgttcatcaatatttacatttgtttgacaatatgcatttgcatttattttacagGTTGTCGAACTGGACTTCCTATACCCCAGTGAGGGAATTCACCAGAGATGGGACAATGGTTACCGGATAACTGCAACTGCTGCAACCTGGGATCAGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC