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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACAATCACTTTTGCCACAAATGCAAGGCCTTAATCAGTACAGTTTGACTGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccgtgttatattctttttaattttgtttactatctatactcctttaaaagaaggtagtggtggtggcagtgaatctgccaccccccatctact...

Basic information

species Oryza sativa
transcript LOC_Os03g31010.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g31010.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G168913_T02 (Zea mays), 5'ss of exon 1
---TCACAATCACTTTTGCCACAAATGCAAGGCCTTAATCAGTACAGTTTGACTGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccgtgttatattctttttaattttgtttactatctatactcctttaaaagaaggtagtggtggtggcagtgaatctgccaccccccatctact-
   |     |   |  ||       |        ||  ||||||  || || ||||||||||||| || |||||||||||   ||||||||||||||||||||||||||  |   ||    | |||   | |||      || |  ||     |  | | ||   | || |    ||  || || ||  ||  |  || |    
AACTTCTTGTATTTAATGTGTTGTTTTATTATTATTTCTCAGTATGGTATGGCTGGTGGGCATCCACATAGGAGCCATCC---CCAAATGCTGACTGACCAAAgtatgtatc-cctttccctttttaagacttttcaagttagcactatcaaatggataaaaaaaaatgttatgtgccatggatttgagacatcatatttgtct

upper sequence: LOC_Os03g31010.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G883871_T01 (Zea mays), 5'ss of exon 6
-TCACAATCACTTTTGCCACAAATG----CAAGGCCTTAATCAGTACAGTTTGACTGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccgtgttatattctttttaattttgtttact-atctatactcctttaaaagaaggtagtggtggtggcagtgaatctgccaccccccatctact---
   |  | || ||  || ||   ||    |  |     | |||  |  | ||| ||  ||||||||| || |||||||||||   ||||||||||||||||||||||||||  |   ||     |||||     |||||   |  |      |   |     | |   | |  |    | | ||  ||| | |      ||  |||   
AGAAAGAGCAGTTA-GCAACTGGTGTTGTCGTGTTGCGACTCAAAAGGGCTTGCCTA-TGGGCATCCACATAGGAGCCATCC---CCAAATGCTGACTGACCAAAgtatgtatcccttt---cccttttaggccttgttcgtttgtgccagattgatgggtcggaacgattcctaaccggattgcttct-ctaatttatataaactttg

upper sequence: LOC_Os03g31010.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G168913_T01 (Zea mays), 5'ss of exon 11
TCACAATCACTTTTGCCACAAATGCAAGGCCTTAATCAGTACAGTTTGACTGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccgtgttatattctttttaattttgtttactatctatactcctttaaaagaaggtagtggtggtggcagtgaatctgccaccccccatctact-
                                       ||  || || ||||||||||||| || |||||||||||   ||||||||||||||||||||||||||  |   ||    | |||   | |||      || |  ||     |  | | ||   | || |    ||  || || ||  ||  |  || |    
---------------------------------------TATGGTATGGCTGGTGGGCATCCACATAGGAGCCATCC---CCAAATGCTGACTGACCAAAgtatgtatc-cctttccctttttaagacttttcaagttagcactatcaaatggataaaaaaaaatgttatgtgccatggatttgagacatcatatttgtct

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|88852485|gb|CI374253.1|CI374253
EST:     TCCATCCCAAATGCTGACTGACCAAA                         TGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
genomic: TCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|33795937|gb|CF323836.1|CF323836
EST:     GGTGGGCATCCTCAAAGGAGCCATCCCATCCCAAATGCTGACTGACCAAA                         TGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
genomic: GGTGGGCATCCTCAAAGGAGCCAT-CCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|86864096|gb|CI332977.1|CI332977
EST:     TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAA                         TTTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATTCAGCAGC
genomic: TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|86535539|gb|CI175745.1|CI175745
EST:     TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAA                         TGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
genomic: TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|86872372|gb|CI341996.1|CI341996
EST:     TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAA                         TGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
genomic: TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|88271636|gb|CI387689.1|CI387689
EST:     TGGTGGGCATCCTCAAA-GAGCCATCCATCCCAAATGGTGACTGACCAAA                         TGTGTGGTATGTGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
genomic: TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|88263292|gb|CI367066.1|CI367066
EST:     GGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAA                         TGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
genomic: GGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|33796204|gb|CF323968.1|CF323968
EST:     GGTGGGCATCCTCAAAGGAGCCATCCCATCCCAAATGCTGACTGACCAAA                         TGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
genomic: GGTGGGCATCCTCAAAGGAGCCATCC-ATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|87027181|gb|CI278213.1|CI278213
EST:     TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAA                         TGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
genomic: TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|86901242|gb|CI326085.1|CI326085
EST:     TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGC-GACTGACCAAA                         TGTTTGGTAT-GGAGGCGCAAATTCTACCAGCATGATGGGAATTCAGCAGC
genomic: TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|88268857|gb|CI377761.1|CI377761
EST:     TGGTTGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAA                         TGTTTGGTATGGGAGGCGCAAATTGTACCAGCATGATGGGAATGCAGCAGC
genomic: TGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
EST: gi|88200375|gb|CI200225.1|CI200225
EST:     GCTGA-TGACCAAA                         GGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC
genomic: GCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGC

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), 69 (downstream exon)
Score: 15

TCACAATCACTTTTGCCACAAATGCAAGGCCTTAATCAGTACAGTTTGACTGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccg ... tccattacagTGTTTGGTATGGGAGGCGCAAATTCTACCAGCATGATGGGAATGCAGCAGCAGCAGCAATTTAACATGCAAGCAAATGCTCAGAACCTGCAACAAGGCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACAATCACTTTTGCCACAAATGCAAGGCCTTAATCAGTACAGTTTGACTGGTGGGCATCCTCAAAGGAGCCATCCATCCCAAATGCTGACTGACCAAAgtatgtgccgtgttatattctttttaattttgtttactatctatactcctttaaaagaaggtagtggtggtggcagtgaatctgccaccccccatctact

- - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccca