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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaaaactaggagatagtccatttttgtttgtt...

Basic information

species Oryza sativa
transcript LOC_Os03g18070.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G074401_T01 (Zea mays), 5'ss of exon 6
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccact-taatgttgaaaaactaggagatagtccatttttgtttgtt---------
 ||||||||   ||||| ||| | || ||||| ||||||||||||||||| || ||||||||||| |||||||||||| ||||       ||||| | |      | ||| | ||||||  ||| ||||||    | |||| |||| || |||||| | |      |||||||||| ||| |         
GTATTTGTTGCTTGGCTGGATATGGTTACATACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGACAGgtg------attatgagtaaagcagttttccaatttgttgatgtttcaag----gtcactgtaatcttcaaaaaccacggttacttccatttttggttggttagaagctt

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G128971_T03 (Zea mays), 5'ss of exon 2
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaaaact---aggagatagtccatttttgtttgtt---
 ||||||||   ||||| ||| | |||||||| ||||||||||||||||| || ||||||||||| |||||||||||||||||       || ||||        | ||| | ||||||  ||| |||||   |    |  || ||| |   |  |    |  | |  |    || ||  || |   
GTATTTGTTGCTTGGCTGGATATGGTCACATACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAGgtg------atcattagcaaagccgttttccaatttgttgatgtttcaatcttcaaaaactagtgtcgtccattttttggttgcttataagcttctgaatgcttac

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G128971_T02 (Zea mays), 5'ss of exon 5
-------------------ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaaaact---aggagatagtccatttttgtttgtt---
                    ||||||||   ||||| ||| | |||||||| ||||||||||||||||| || ||||||||||| |||||||||||||||||       || ||||        | ||| | ||||||  ||| |||||   |    |  || ||| |   |  |    |  | |  |    || ||  || |   
TTCCTGCTGGTGTGTGCAGGTATTTGTTGCTTGGCTGGATATGGTCACATACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAGgtg------atcattagcaaagccgttttccaatttgttgatgtttcaatcttcaaaaactagtgtcgtccattttttggttgcttataagcttctgaatgcttac

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA03G07570.1 (Glycine max), 5'ss of exon 6
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaaaactaggagatagtccatttttgtttgtt--
|| |||||||||||| | ||||| || || |||||||| || ||||||||||| |||||  | |||||||| |||||| |||||     | ||     ||   |   ||| | |        |   | ||    | |     | | |||||  |  |||| | |    |  | |  ||  |  
ATTTTTGTTATGTGGTTGGATTTGGTGACTTATTTGCATCACCATGGCCATGAAGACAAATTACCTTGGTATCGTGGAGAGgtatcctttctttcctttttctttcttttccaagaaaatgtttgcttaacttggtctttccacttttgaatta--aggataaaacttagatgtaattcctta

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G29630.1 (Glycine max), 5'ss of exon 6
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgat-tcaaggatggccacttaatgttgaaaaactaggagatagtccatttttgt-ttgtt-
|| |||||||||||| | ||||| || || |||||||| || ||||||||||| |||||| | |||||||| |||||| |||||  | || |  ||  || | ||  | |  |    | ||||| | |  |   ||| |  |  |  ||   ||  ||   | |||    ||||  | ||||| 
ATTTTTGTTATGTGGTTGGATTTGGTGACTTATTTGCATCACCATGGCCATGAAGACAAGTTACCTTGGTATCGTGGAGAGgta--ttatttctttccttttgtgtttcttttccaagaaaatgttgtttaacttggtctttccaccttttgaa-ttactcgttaggtatttttcatgttgtta

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G43210.1 (Glycine max), 5'ss of exon 5
------------------ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggcc--acttaatgttgaaaaac-taggagatagtccatttttgtttgtt
                  ||||| ||||||||| | ||||| || || ||||||||||||||||||||||| |||||  | |||||||||||||||||||||      ||| || |  || |   | |  |       | || |  |    || |   || || | |||  |    || ||| |      |  |   |||||
AATTTCTTGGAATTGAAGATATTCGTTATGTGGTTGGATTTGGTGACTTATTTGCACCATCATGGCCATGAAGACAAATTACCTTGGTACCGTGGAAAGGtatccttcattctttaaagtct--ttcttatgaaaaggactggtctatttgtgtcttgacatacttttgttatgtgtatgagtttaattttcatgcattgtt

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G18350.1 (Glycine max), 5'ss of exon 6
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaaaactaggagatag-tccatttttgtttgtt--------
||||| || |||||| | ||||| || || ||||||||||||||||||||||| | |||  | |||||||| ||||||||||||  |   ||||||    ||      ||    | || |||||| |   | ||      | ||||   | ||  |||   | |  |  ||  || || ||         
ATATTCGTCATGTGGTTGGATTTGGTGACTTATTTGCACCATCATGGCCATGAAGGCAAATTGCCTTGGTATCGTGGAAAGgtatctttcattatttcaagtcctttcttttcttatgaaaatgact--ggtataatg--tcaatgcatagaatttagtttacatctttatccttcttcgtgttgaacag

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G11170.1 (Arabidopsis thaliana), 5'ss of exon 6
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaa--aactaggagatagtccatttttgtttgtt-------
|||  ||| |||||| | || ||||| || ||  |||| || ||||| ||||| || |||||||||||||||||||| ||||||||  | ||     ||| | ||  |   || ||  |  |  |        |   |  |||| ||| ||   |||| |    ||   |   |   | |          
ATAAATGTAATGTGGTTGGACTTTGTGACTTACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaatacat-----attctctgcttccactgttctttgactacatcgctctt-tcttttaaggttaaagccaactggtgtgtaaatctcatgattctcccaaaacag

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 6
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaag-gatggccacttaatgttgaaaaactaggagatagtccatttttgtttgtt--------
|||||||| |||||| | || || ||||| || |||||||| ||||| ||||| |||||||| |||||||| ||||||||||||   || ||         ||    ||  |  |||||||  || | |   ||  | ||||   |||||  | | |   | |   | ||| |   ||            
ATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACATGAAGACAAGCTCCCTTGGTATCGTGGAAAGgtatgcaaaatc--------tac---ttcaccttttgtaatcgagttacctgagagacact-gttgttgtgagaatcacaaacgcttcatgtactttccccaaacacag

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv13s0067g01120.t01 (Vitis vinifera), 5'ss of exon 6
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaatt--gtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaaaactaggagatagtc--catttttgtttgtt------------------------------------
|| || || |||||| | ||||| || || || ||||| || ||||||||||| || |||||||||||||| ||||||||||||   |||    ||  |   |  | ||  ||||  || ||  | ||||   | || | ||  |  |   |||||      | || |   || ||  |  | ||                                    
ATTTTCGTCATGTGGTTGGATTTAGTGACTTACTTGCATCACCATGGCCATGAAGAGAAGCTTCCTTGGTATCGTGGAAAGgtatcaaattcagtttctctagattaggcctgctgattatatttcattcttcgctg-caacaaagagggaaaaaagagaatgctaataaacaattcagcattttaactgaaaacccgacttctggctctgtttttcacag

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 6
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaa--aactaggagatagtccatttttgtttgtt--
|| |||||||||||||| |||||||| || ||| |||| || ||||| ||||| || || ||||||||||| ||||||||||||  |   || ||   || ||  | |||  |  || | ||| |       || |   |  || | |||||  |||| | |  |   |||    |  |  ||  
ATTTTTGTTATGTGGCTGGATTTTGTGACTTATCTGCATCACCATGGTCATGATGATAAACTTCCTTGGTATCGTGGAAAGgtatgt--catcatgctttctactgtttt--tggttttcaataaaattttcatagttccagaaagatgaaactaacttgtatgtttaccaagagtagtcattgt

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|88847647|gb|CI018338.1|CI018338
EST:     ATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG                         GAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGG
genomic: ATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataata ... gctctattagGAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGG
EST: gi|29684208|gb|CB680483.1|CB680483
EST:     ATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG                         GAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGG
genomic: ATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataata ... gctctattagGAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGG
EST: gi|29618634|gb|CB623646.1|CB623646
EST:     ACTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG                         GAGTGGAGCTATCTGCGAGGAGGATTGACAACACTTGATCGGGACTACGGG
genomic: ATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataata ... gctctattagGAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGG
EST: gi|88965936|gb|CI006724.1|CI006724
EST:     CCATCATGGCCATGAGGACAAGCTTCCTT-GTACCTTCGGAAAG                         GAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGG
genomic: CCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGT-GGAAAGgtaaataata ... gctctattagGAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGG
EST: gi|89195878|gb|CI007297.1|CI007297
EST:     ATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG                         GAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGG
genomic: ATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataata ... gctctattagGAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGG

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: 67 (upstream exon), 75 (downstream exon)
Score: 41

ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataata ... gctctattagGAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGGTGGATCAACAACGTACACCATGACATTGGAACCCATGTCATTCATCATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaaaactaggagatagtccatttttgtttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT