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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCAACAACATGCATTCTGCCAGTTTGTAACTGGTGCTCCTCGGCTTCCGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattcttggtatatcttattagcatgttataacgtatgaatattgtcgcctcattttgggtgatataactttgttgttgcttttgatcattag

Basic information

species Oryza sativa
transcript LOC_Os02g01170.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01170.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G374574_T02 (Zea mays), 5'ss of exon 15
AGAGCAACAACATGCATTCTGCCAGTTTGTAACTGGTGCTCCTCGGCTTCCGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct-tggtatatct-tattagcat--gttataacgtatgaatattgtcgcctcattttgggtgatataacttt-gttgttgct------tttgatcattag---
 ||||| || ||||| ||||||||||||||||| ||||||||||||||||| | |||||| || ||||||||||  ||||||||||||||||||||||||||| | ||   |||| ||||| |  | ||||  | ||||| |     || |   | ||| ||| ||  |||| | | ||| |  ||  ||      |||||| |||     
TGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCCTTAGCCCCAAGCTTACTATAGTTAGGAAGgtaccttttcatggtctatctatcgtggcatttgctataatg---acatgtgcacacct-attctgcttgatgttatttttggggtaactcggtgttttgattattgccag

upper sequence: LOC_Os02g01170.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT4G38600.1 (Arabidopsis thaliana), 5'ss of exon 15
AGAGCAACAACATGCATTCTGCCAGTTTGTAACTGGTGCTCCTCGGCTTCCGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacatt-cttggtatatcttattagcatgttataacgtatgaatattgtcgcctcattttgggtgatataactttg--ttgttgcttttgatcattag
||| || ||    || |||||||| ||||||||||| |||||| ||||||| |||||||| |||||||  || || || |||||||| || || || ||||||| |   |||   ||   ||   ||    || |    | |    |     |     ||    |  || ||  | ||       ||||||| || ||  
AGATCAGCAGAGGGCTTTCTGCCAATTTGTAACTGGAGCTCCTAGGCTTCCTCCTGGTGGCTTAGCTGTTCTGAACCCAAAGCTTACGATTGTGAGAAAGgtaaaaaaactttaaatcatttgcaagtcatttttgtaatttagccaccaaggatatgttagaaggcatctatgtgtgggcaagggcttttgctcttttt
















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|29670954|gb|CB667229.1|CB667229
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|88348058|gb|CI637519.1|CI637519
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|29678536|gb|CB674811.1|CB674811
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|29664291|gb|CB660566.1|CB660566
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|163923587|gb|EG711528.1|EG711528
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|88377761|gb|CI637895.1|CI637895
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|88689684|gb|CI733260.1|CI733260
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|29678538|gb|CB674813.1|CB674813
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|29670955|gb|CB667230.1|CB667230
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|58594862|gb|CF993170.1|CF993170
EST:     CCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|66922255|gb|CX109103.1|CX109103
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|33793172|gb|CF322467.1|CF322467
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAA-TATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|29640685|gb|CB645694.1|CB645694
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|29628307|gb|CB633318.1|CB633318
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCTGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
EST: gi|25807633|gb|CA763594.1|CA763594
EST:     CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAG                         CACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT
genomic: CGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCT

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: 73 (upstream exon), 74 (downstream exon)
Score: 91

AGAGCAACAACATGCATTCTGCCAGTTTGTAACTGGTGCTCCTCGGCTTCCGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattct ... tgatcattagCACCCCTCAAGTGCGGTGAATACTTCAAATATCGCTGGAGTTACAGAGTCTGCAGATGATGATCTGCCAAGTGTTATGACATGTGCTAATTATCTTAAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCAACAACATGCATTCTGCCAGTTTGTAACTGGTGCTCCTCGGCTTCCGCCTGGTGGTTTAGCTGCCCTTAATCCCAAGCTTACTATAGTTAGGAAGgtaacattcttggtatatcttattagcatgttataacgtatgaatattgtcgcctcattttgggtgatataactttgttgttgcttttgatcattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT