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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacataatgattaatcatgcttcaactttttgtagctaccagtctgccagcatggtaacttgagaagtcgactaacagttaactcttacgtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGCCGACTGTTCGGTTTGTTTCTAGGATGTTCCACCCAAATA

Basic information

species Oryza sativa
transcript LOC_Os07g07240.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07240.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G022206_T02 (Zea mays), 3'ss of exon 2
ccacataatgattaatcatgcttcaactttttgtagctaccagtctgccagcatggtaac-ttgagaagtcgactaacagttaactct-tacg-tatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGCCGACTGTTCGGTTTGTTTCTAGGATGTTCCACCCAAATA
   |     |    | | ||||   |  |||      |     | ||| |  ||| || | ||| |||||  ||| ||  || ||| | |     |||| |||||||||||||||||||||||||||||||||||||||| || |||||||| || ||||||||||| || ||||||||||| || ||||| |
tttctcctagccctagcgtgctgggatattt---gaatggttatgtgctattatgttagcattgcgaagttcactgactattgactgtgtgtaacatctatagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGGTTCGTCTCTAGGATGTTTCATCCAAACA

upper sequence: LOC_Os07g07240.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074479_T04 (Zea mays), 3'ss of exon 2
ccacataatgattaatcatgcttcaactttttgtagctaccagtctgccagcatggtaac-ttgagaagtcgactaacagttaactctta--cgtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGCCGACTGTTCGGTTTGTTTCTAGGATGTTCCACCCAAATA
   |     |  | | ||||||   | ||||   |  |  |  | ||| |  |||  | | |||  ||||  ||| ||  || ||| |       || |||||||||||||||||||||||||||||||||||||||||| || |||||||| || |||||||| ||||| ||||||||||| || |||||||
tttcccttagccttagcatgctgagattttt---aaatggctttgtgctattatgtcagcattgcaaagttcactgactattgactgtatgttacatatgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTACCCAAACAAGCCACCAACTGTTCGATTTGTCTCTAGGATGTTTCATCCAAATA

upper sequence: LOC_Os07g07240.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ23951 (Selaginella moellendorffii), 3'ss of exon 2
ccacataatgattaatcatgcttcaactttttgtagctaccagtctgccagcatggtaacttgagaagtcgactaacagttaactcttacgtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGCCGACTGTTCGGTTTGTTTCTAGGATGTTCCACCCAAATA
                                          ||  ||||  |      |||      ||   | | ||  || | ||     |    ||| |||||||||||||| || ||||| || || || ||||||||||| ||||| | ||| |||||||| || | ||||||||| || || |
------------------------------------------gtgagccaaaact-cgtctttttccttcttgtgatag--aattttttttcgttgtcagGTACGTTCAAGCTTACGTTACAGTTCACGGAGGACTATCCCAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACA

upper sequence: LOC_Os07g07240.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 2
ccacataatgattaatcatgcttcaactttttgtagctaccagtctgccagcatggtaacttgagaagtcgactaacagttaactcttacgtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGCCGACTGTTCGGTTTGTTTCTAGGATGTTCCACCCAAATA
                                          ||  ||||  |      |||      ||   | | ||  || | ||     |    ||| |||||||||||||| || ||||| || || || ||||||||||| ||||| | ||| |||||||| || | ||||||||| || || |
------------------------------------------gtgagccaaaact-cctctttttccttcttgtgatag--aattttttttcgttgtcagGTACGTTCAAGCTTACGTTACAGTTCACGGAGGACTATCCCAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACA

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|58589089|gb|CF987397.1|CF987397
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|87030405|gb|CI252682.1|CI252682
EST:     TTCGGGCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: TTCGGGCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|88370680|gb|CI592446.1|CI592446
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|33829483|gb|CF340565.1|CF340565
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|87018548|gb|CI252302.1|CI252302
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|58589326|gb|CF987634.1|CF987634
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|33815914|gb|CF333803.1|CF333803
EST:     GTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATTCCAACAAGCCGC
genomic: GTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|396941349|gb|HO188558.1|HO188558
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|58602468|gb|CK012996.1|CK012996
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|58594410|gb|CF992718.1|CF992718
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|86601347|gb|CI251721.1|CI251721
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|58597267|gb|CK007795.1|CK007795
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|88390727|gb|CI610953.1|CI610953
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|86592637|gb|CI253318.1|CI253318
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|15008457|gb|AU222845.1|AU222845
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|86599452|gb|CI251410.1|CI251410
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|33661350|gb|CF292317.1|CF292317
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|88826116|gb|CI776681.1|CI776681
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|88727870|gb|CI749382.1|CI749382
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|88364559|gb|CI612374.1|CI612374
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|218486911|gb|FG967738.1|FG967738
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|88571683|gb|CI663056.1|CI663056
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|3767492|gb|AU031602.1|AU031602
EST:     CCCGGATGATACCCCTTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|27577517|gb|CB000212.1|CB000212
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|88721800|gb|CI745099.1|CI745099
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|88444098|gb|CI594471.1|CI594471
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|88440712|gb|CI693273.1|CI693273
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|33823815|gb|CF337714.1|CF337714
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|218500131|gb|FG955693.1|FG955693
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|87023876|gb|CI288229.1|CI288229
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|55409265|gb|CV721641.1|CV721641
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
EST: gi|7608720|gb|AU090501.1|AU090501
EST:     GCCGGATGATACGCCGTGGGACGGAG                         GCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC
genomic: GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGC

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: 74 (upstream exon), 68 (downstream exon)
Score: 122

GCCGGATGATACGCCGTGGGACGGAGgtgaggcttg ... gtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGCCGACTGTTCGGTTTGTTTCTAGGATGTTCCACCCAAATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacataatgattaatcatgcttcaactttttgtagctaccagtctgccagcatggtaacttgagaagtcgactaacagttaactcttacgtatctgtagGCACGTTCAAGCTTACCTTGCAGTTTACAGAAGATTATCCCAACAAGCCGCCGACTGTTCGGTTTGTTTCTAGGATGTTCCACCCAAATA

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