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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcatctttttacactgcagtattctacatactatgacatagttgatcataacacaacatacatgaaaagaacaacctactcgtactatcttgtttttgtagctgcccttatgtcaggtcagcataacccctgtatgtgtgtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGACGATGCTGTTGCGGCTGCGGAGGAAGCAGCGTTCTGCAAAGCCTGCGCAC

Basic information

species Oryza sativa
transcript LOC_Os09g33790.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33790.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G868664_T01 (Zea mays), 3'ss of exon 3
----gtatttcatctttttacactgcagtattctacatactatgacatag-ttgatcataacacaacatacatgaaaagaacaac-ctactcgtactatcttgtttttgt--------------agctgcccttatgtcag--gtcagcataaccc-------ctgtatgtgtgtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGACGATGCTGTTGCGGCTGCGGAGGAAGCAGCGTTCTGCAAAGCCTGCGCAC
       ||    |||||| | || | | | | |   |       || |  || |   |  |||     | || | | |    || |||   | || ||||| ||||| |              |  | |  | |   ||   |||   || | |         || || | | ||||| |||||||||||||| || || ||||| ||||   | || ||||| || |  || ||||||||||| || || |||||||| || |||||||||||||||||||
gtaaactttctcccttttttctctacggaagttttgttgtacctgcacaaatttaaagtggcacttttcaaattatatggttcacactaactgcaccatcttttttttcttttgaaatcaactaaaatacattgaaaacaatcgtctatattaactgatgcaattgcatctttttgagt-tagGCATACAGAGATGCCACGGGCACAGCACAGTTACATGAGGGGCGCAGGGAAGATGCTGTTGCAGCCGCAGAGGAAGCTGCATTCTGCAAAGCCTGCGCAC
















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|29688869|gb|CB685144.1|CB685144
EST:     GAACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACGGAGAG                         GCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
genomic: GAACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACGGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
EST: gi|86534902|gb|CI175108.1|CI175108
EST:     GAACAGACGGAGAG                         GCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
genomic: GAACAGACGGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
EST: gi|89168516|gb|CI038870.1|CI038870
EST:     TTCTGAGAGGAACAGACGGAGAG                         GCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
genomic: TTCTGAGAGGAACAGACGGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
EST: gi|24468750|gb|CA305699.1|CA305699
EST:     AACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACNGGAGAG                         GCATACAGAGAGGCTACATGGCACGGCACCAGTGCACGAGGGCCGTAACG
genomic: AACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGAC-GGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTAC-TGGCACGGCACCAGTGCACGAGGGCCGTAACG
EST: gi|87018651|gb|CI254359.1|CI254359
EST:     GAACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACGGAGAG                         GCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
genomic: GAACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACGGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
EST: gi|86486459|gb|CI129092.1|CI129092
EST:     GAGGAACAGACGGAGAG                         GCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGTCCGTAACGAC
genomic: GAGGAACAGACGGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
EST: gi|88224728|gb|CI224577.1|CI224577
EST:     GAACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACGGAGAG                         GCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
genomic: GAACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACGGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
EST: gi|112785501|gb|EE590824.1|EE590824
EST:     GAACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACGGAGAG                         GCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
genomic: GAACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACGGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGAC
EST: gi|86597209|gb|CI280346.1|CI280346
EST:     ATCGAGTGATTCTGAGAGGAACAGACGGAGAG                         GCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTTAACGA
genomic: ATCGAGTGATTCTGAGAGGAACAGACGGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCG-TAACGA

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: 73 (upstream exon), 44 (downstream exon)
Score: 12

GTTGGTGTGGAGAAGTTCGCAATGTTATTTATTCTGACAATGGAACTGTAACCGTGGTTTATCGAGTGATTCTGAGAGGAACAGACGGAGAGgtatttcatc ... gtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGACGATGCTGTTGCGGCTGCGGAGGAAGCAGCGTTCTGCAAAGCCTGCGCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtagctgcccttatgtcaggtcagcataacccctgtatgtgtgtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGACGATGCTGTTGCGGCTGCGGAGGAAGCAGCGTTCTGCAAAGCCTGCGCAC
                          gcataac  putative branch site (score: 12)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcatctttttacactgcagtattctacatactatgacatagttgatcataacacaacatacatgaaaagaacaacctactcgtactatcttgtttttgtagctgcccttatgtcaggtcagcataacccctgtatgtgtgtgagtgtagGCATACAGAGAGGCTACTGGCACGGCACCAGTGCACGAGGGCCGTAACGACGATGCTGTTGCGGCTGCGGAGGAAGCAGCGTTCTGCAAAGCCTGCGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG