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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacacatttgattgtcacacgaaattaagtgcactggagtccatgattttagattttgcgtatgactaattaataaatgttccccttttctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAG

Basic information

species Oryza sativa
transcript LOC_Os02g05630.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 1
--taacacatttgattgtcacacgaaattaagtgcactggagtccatgattttagattttgcgtatgactaattaataaatgttccccttttctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAG
  |    |||||     | | |  |||  |     |    |    |  | |  || |       |||| |     | |  |  |      || | || | ||| | ||  | || ||||| ||||||||||| ||  ||||||| || ||  |||||||||| ||||| || ||||| ||||| |||||||||||||| || 
tctctggcattt--cctttaaaaaaaaaaagaaagaaaaaaactaaacaatgaagctgcatgagatgattgtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA

upper sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 2
--taacacatttgattgtcacacgaaattaagtgcactggagtccatgattttagattttgcgtatga-ctaattaataaatgttccccttttctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAG
   |  || ||  | |||        ||    |  | |    || |  |   ||    | ||  | || ||   ||| | | ||      | |    | ||||| | || || |||||||| || || ||||| ||| |||| ||||||||| |||||||||| ||||| || ||||| ||||| ||||||||||| ||||||
ttgaggaccttataatgtttggttttatctt-tctaatatcatctacaacaataagagt-gcacaggatcttcctaacata-gtgtgagatgttgtctaacagTCATAATGGGAAGTTCAGCTACGGATATGCTAGTTCTCCCGGGAAAAGGTCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGAAGGAGAG
















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|5003494|gb|AU068643.1|AU068643
EST:     CGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: CGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|5803440|gb|AI978410.1|AI978410
EST:     CGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: CGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29668036|gb|CB664311.1|CB664311
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29639786|gb|CB644795.1|CB644795
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|58670044|gb|CK058730.1|CK058730
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29666851|gb|CB663126.1|CB663126
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29688008|gb|CB684283.1|CB684283
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|88445125|gb|CI589603.1|CI589603
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|33675133|gb|CF303372.1|CF303372
EST:     GCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29686520|gb|CB682795.1|CB682795
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|44671917|gb|CR285351.1|CR285351
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29640127|gb|CB645136.1|CB645136
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29662047|gb|CB658322.1|CB658322
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC

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: 64 (upstream exon), 73 (downstream exon)
Score: 41

CGGGTCGGTCGTCTTGCTGGTGGCTGGAGGGCACGGAGGAGTTGGAGGAGGAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttagattttgcgtatgactaattaataaatgttccccttttctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAG
                                 tgttccccttttctgt  CT-rich tract
                tatgactaattaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacacatttgattgtcacacgaaattaagtgcactggagtccatgattttagattttgcgtatgactaattaataaatgttccccttttctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - -tgattgt
- - - - - - - - - cacgaaa
- - - - - - - - - - - - - - - tgcactg
- - - - - - - - - - - - - - - - - - - -gtccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - -attttgc