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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgattggtccaacaaacaatggtgctgaattgtctagtgcattaagacctcaatccaaatttaccatctaattgccttttcatttgtatctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGGTTCCCGGCTGCCTACGTGGAGAGGCGTGAAAATATCCCGCCAAACAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g32460.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g32460.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G179459_T01 (Zea mays), 3'ss of exon 9
-atcgattggtccaacaaacaatggtgctgaattgtctagtgcattaagacctcaatccaaatttaccatctaattgccttttcatttgtatctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGGTTCCCGGCTGCCTACGTGGAGAGGCGTGAAAATATCCCGCCAAACAAAG
 |   ||| | |   | |||||          |   | | |    |  ||      |   | | ||  ||   ||     ||   | |||  |||| | |||||||||| || || ||||| ||||||||||||   |||  ||| || ||||| ||||||||||| || |||||||| || |||||||| || || ||||
aacgaattagcctgtccaacaacaaaaaaagttaacccactat-ctgtgagtagtgttttactgtatgattgcatccttgttctctctgtgcctgcaccagATTGCTCCCAACGGCTGGGCGGAAGGAGAATGCCGAGGGAAGGCTGGCTGGTTTCCGGCTGCCTATGTTGAGAGGCGCGAGAATATCCCCCCGAATAAAG
















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|88519773|gb|CI447427.1|CI447427
EST:     TTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: TTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|88485339|gb|CI422610.1|CI422610
EST:     TGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: TGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|89172885|gb|CI040778.1|CI040778
EST:     AGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: AGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|88508762|gb|CI436268.1|CI436268
EST:     TTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: TTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|88265548|gb|CI376450.1|CI376450
EST:     TTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: TTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|86831642|gb|CI301492.1|CI301492
EST:     CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|86477363|gb|CI119996.1|CI119996
EST:     CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|89167661|gb|CI109062.1|CI109062
EST:     CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCCCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|2431289|gb|C73709.1|C73709
EST:     ATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAA-GAGAATGCAAGGGGGTGGCAGGATGG
genomic: ATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|86827427|gb|CI272824.1|CI272824
EST:     CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|86433112|gb|CI093455.1|CI093455
EST:     CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|86431539|gb|CI085150.1|CI085150
EST:     CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|88420470|gb|CI562104.1|CI562104
EST:     TTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: TTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|3763693|gb|AU030445.1|AU030445
EST:     CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGNGAATGCAAGGGGGTGGCAGGATGG
genomic: CAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
EST: gi|88409439|gb|CI561925.1|CI561925
EST:     TAATTGTTGGTGATTATGTCGTTGTTCGTCAG                         ATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG
genomic: TAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGG

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), 51 (downstream exon)
Score: 12

GCGGTGCATAACTTCAATGGTACCACAGAAAAGGAGTTGAGTTTAATTGTTGGTGATTATGTCGTTGTTCGTCAGgtcagtgtcc ... tctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGGTTCCCGGCTGCCTACGTGGAGAGGCGTGAAAATATCCCGCCAAACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagacctcaatccaaatttaccatctaattgccttttcatttgtatctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGGTTCCCGGCTGCCTACGTGGAGAGGCGTGAAAATATCCCGCCAAACAAAG
                      atctaat  putative branch site (score: 12)
                                             tctgctct  putative PPT
                                 ttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcgattggtccaacaaacaatggtgctgaattgtctagtgcattaagacctcaatccaaatttaccatctaattgccttttcatttgtatctgctctagATTGCTCCGAATGGTTGGGCCGAAGGAGAATGCAAGGGGGTGGCAGGATGGTTCCCGGCTGCCTACGTGGAGAGGCGTGAAAATATCCCGCCAAACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - -caacaaa
- - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - -aatccaa