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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatacgatgatctgttttcttattttctattggcactggattctcaaaaggattttcttgctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCTTCAGTGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTT

Basic information

species Oryza sativa
transcript LOC_Os10g25130.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 3
gtaaatacg-atgatctgttttcttattt-tctattggc------actggattctcaaaaggattttcttgctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCTTCAGTGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTT
||||||    || | | | |   |||| |  || |||||      ||||| || || |||  ||||| ||||||  | ||||||| ||||| || ||||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||||||  | || ||||||||| |
gtaaatttatataaccagctactttatctgccttttggccaagtaactggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT

upper sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 10
--gtaaatacgatgat--ctgtt---ttcttattttctattggcactggattctcaaaaggattttcttgctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCTTCAGTGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTT
    ||  || |   |  ||||    | ||| |  ||||     |  || || |       | | |  | |||   | |||||||||||| |||||||| ||||||||||| ||||||||| ||||||| |||| | ||   || ||||| ||||| |||||| |||| || |||||  |
gtaaaagaacaacttttactgtccaatgcttgtcatctaa-aaaatggggtttttgtttttaatattcttctgttgatagGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT

upper sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G17290.1 (Arabidopsis thaliana), 3'ss of exon 10
-------------gtaaatacgatgatctgtt-----ttcttat--tttctattggcactggattctcaaaaggattttcttgctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCTTCAGTGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTT
               ||||    |  ||  ||     |||| ||  || | || || |     |    |||  || ||  ||  |    ||||| || ||||| || ||||| |||||||| || ||||||||| ||||||| |||| | ||   || ||||||||||| |||||| |||| || |||||  |
gtttgatacaaaaacaaatctcttagtcaattgataattctgatcattgcgatgggaaactagtcagaaaactgaattcattatttctgacagGGTACTATGGAGAGTGTGGGAAAAGAGGTGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAGCAGATATACAAAATGGCTTCTGTGAATCT

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|88269769|gb|CI381067.1|CI381067
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATTATGGTGAATGTGGCAAAAAGAGGAGGCTACATGG
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAA-GAGGAGGCTACATGG
EST: gi|29668876|gb|CB665151.1|CB665151
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
EST: gi|487302|gb|D29993.1|D29993
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATNATGGTGAATGTGGC
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGC
EST: gi|86909087|gb|CI302726.1|CI302726
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
EST: gi|218502337|gb|FG952302.1|FG952302
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
EST: gi|38481162|gb|CF965251.1|CF965251
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
EST: gi|29666343|gb|CB662618.1|CB662618
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
EST: gi|163926601|gb|EG713617.1|EG713617
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATTATGGTGAATGTGGCAAA-GAGGAGGCTACATGGAGATTACTGGCT
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
EST: gi|29666342|gb|CB662617.1|CB662617
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
EST: gi|13165185|gb|AU173982.1|AU173982
EST:     ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGG                         GATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT
genomic: ATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCT

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: 66 (upstream exon), 74 (downstream exon)
Score: 212

GTTGACAACAAGAAATTTAACTCTTTCAAGAAGATAGCGAGATCCATGGGATACAACGAGGATGATCTCCCTTTAGTATCATTTCAATCTGTTTCTAAGGgtaaatacga ... ctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCTTCAGTGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttattttctattggcactggattctcaaaaggattttcttgctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCTTCAGTGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTT
                                           tgctgac  putative branch site (score: 212)
                                     ttttcttgct  CT-rich tract
     tattttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatacgatgatctgttttcttattttctattggcactggattctcaaaaggattttcttgctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCTTCAGTGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT