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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcatttcttctaatattattcagaaaaaacttttcacagttctttagactgcacaatgcaatggaaataatcaattctaccagtacgtcttcagtcttcactaacttgtgatttggtaaaatcctcag

Basic information

species Oryza sativa
transcript LOC_Os05g07130.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07130.2 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G021846_T02 (Zea mays), 5'ss of exon 19
ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatc-atttcttctaatattattcaga-aaaaacttttcacagttctttagactgcacaatgcaatggaaataatcaattctaccagtacgtcttcagtcttcactaacttgtgatttggtaaaat----cctcag-------------------------
 ||||| |||||||||||  ||||||| || ||||||||||||||||||||||| |||||||| |||||||  || | ||   |||||||  ||| |||| ||||| | | || |||| |||    | |  |    | | |   |  |  | |       |   | |  |    | ||  | ||  | |   ||  ||     ||  |                          
GTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaactatagtttctaat--tatacagacaaaaaatctccatagtttttt--tttcctaagaaaagtcgtgctggtttacttggtttttgtctgtcaaactatgacagatttcagttcccgtgtaactataccctaacagctgatgtcataataacccttag

upper sequence: LOC_Os05g07130.2 (Oryza sativa), 5'ss of exon 20
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 20
ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcatttcttctaatattattcagaaaaaacttttcacagttctttagactgcacaatgcaatggaaataatcaattctaccagtacgtcttcagtcttcactaacttgtgatttggtaaaatcctcag
||| || || |||||||||||| |||| |||||||| |||||||| || ||||||||||| || ||  ||| |  || | ||||||| |  | |  |    ||    |  ||    | | ||     | |  || |     | |||  |                                                      
ATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTACCTTGATGTAATCCAACGgtatgttcttctcttctacttctttctacgtgaagtcataaactaaacctcaggaaa-atatcgctactttgacaatgcag-----------------------------------------------------
















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|58611022|gb|CK038734.1|CK038734
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
EST: gi|86850852|gb|CI338828.1|CI338828
EST:     ATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGGACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCACGTAGTCG
genomic: ATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCA-GTAGTCG
EST: gi|29629510|gb|CB634519.1|CB634519
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
EST: gi|29616012|gb|CB621024.1|CB621024
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
EST: gi|16578926|gb|BI813021.1|BI813021
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGCGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
EST: gi|86838836|gb|CI330278.1|CI330278
EST:     ATCGATACCCCCGTGGAGAATCTTACATTGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGGTCG
genomic: ATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTA-GTCG
EST: gi|29612782|gb|CB617795.1|CB617795
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
EST: gi|29615977|gb|CB620989.1|CB620989
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
EST: gi|86853669|gb|CI330520.1|CI330520
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGGTAGAACGCCAGCGAGCACCAGTAGTCGT
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
EST: gi|88844562|gb|CI020409.1|CI020409
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGAAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCG
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGG-AACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCG
EST: gi|29615975|gb|CB620987.1|CB620987
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
EST: gi|29616052|gb|CB621064.1|CB621064
EST:     TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
genomic: TTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT
EST: gi|86869030|gb|CI335597.1|CI335597
EST:     CCCCCGT-GAGAATCTTACCTGGATGTGATTCAGAG                         ACTGGAACCTGTTATCATTGAGCTA-AACGCCAGCGAGCACCACTAGTCGT
genomic: CCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGT

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: 69 (upstream exon), 64 (downstream exon)
Score: 48

ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcat ... aaatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAGgtttaatcatttcttctaatattattcagaaaaaacttttcacagttctttagactgcacaatgcaatggaaataatcaattctaccagtacgtcttcagtcttcactaacttgtgatttggtaaaatcctcag

- - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - GGAGAA