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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcatatgcatatgtttattctgatgtggcttgttttttttcatggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT

Basic information

species Oryza sativa
transcript LOC_Os03g58040.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 4
gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcat----atgcatatgtttattctgatgtggcttgtttttttt----catggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
|||||||||||||   |||| | ||||    ||||||  |||||| |||  ||    |   ||||||||||||| || |||| | |||| |||     ||||||| |||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| ||||| 
gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgtttattctaatatggcctattttgtttgctttatggatgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG

upper sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 3
gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcatatgcatatgtttattctgatgtggcttgttttttttcatggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
          |||  | | | |    ||  || |||      | | |   | | |         | ||||  | ||   | |  |  |  |    |  |||||||||| ||||| ||||| ||||||||||| || |||||  |||| |||||||| || |||||||||||  ||
---------gtttcgaaaacatgatcttgaagtcttcatcttgtattttacgtgt---------tgttcttgtctgaaatatagtgatgaaaattttcagACAATGGCTTGGATTCTTGATGAATACTCAAAATTCCATGGACATTCTCCTGCTGTTGTCACTGGAAAACCCATT

upper sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcatatgcatatgtttattctgatgtggcttgttttttttcatgga---tgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
            | | ||  ||||| ||    || ||    | |  |     | |   | | |  |  |   | |    | |||   ||  ||||   || |||||||||| ||||| ||||| |||||||| ||||||||||| || || ||||| || ||||||||||||||  ||
-----------gttcttaaactctc-ttcagaacgtttccaaaatgttc-tgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT

upper sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 5
-gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcatatgcatatgtttattctgatgtggcttgttttttt-tcatggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
 |              |  |  |   || |  |  ||   ||   ||     || || |     |    ||  |||  || ||| || | |  | ||   |||| ||||| |||||||| || || ||||| || |||||||| || ||||||||||||||||||||||| ||| ||
agaaggaaaaaaaaaaaagttatggtatctttggtttgaatgttcaacca-tatttgaactaactgtggcttttgtttctggttcttgtgttgttga-acagACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATT

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|29679310|gb|CB675585.1|CB675585
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|58609006|gb|CK037039.1|CK037039
EST:     TTGGCATTCATACAGATGTTCCAGCTCCCGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAA
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAA
EST: gi|66915471|gb|CX102319.1|CX102319
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|88428743|gb|CI599459.1|CI599459
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTT-ATGGTTATTCAC-T
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|29673988|gb|CB670263.1|CB670263
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|29674431|gb|CB670706.1|CB670706
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|163928511|gb|EG711396.1|EG711396
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|88314120|gb|CI602452.1|CI602452
EST:     CATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: CATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
EST: gi|33675066|gb|CF303305.1|CF303305
EST:     TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAG                         ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT
genomic: TTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCT

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: 34 (upstream exon), 68 (downstream exon)
Score: 12

CGAGCTAGAGCGACTTACCCGTGTTTTCACCCAGAAAATCCACGACTTGATTGGCATTCATACAGATGTTCCAGCTCCAGATATGGGAACCAACTCTCAGgttattttcc ... atggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataggcatatgcatatgtttattctgatgtggcttgttttttttcatggatgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
                     ttctgat  putative branch site (score: 12)
                                cttgttttttttcat  putative PPT
                                 ttgttttttttcat  TA-rich tract