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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattttcaaacgagtattggttttatcctgtctgaagcagctaacagttaatgtcttgtcacatttcttatttttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACTTCATATGGCAGCTTTGAATGGTCATTTTGATTGCATGCAATTGTTGATT

Basic information

species Oryza sativa
transcript LOC_Os10g37730.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37730.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AC194389.3_FGT001 (Zea mays), 3'ss of exon 4
gtatgtattttcaaacgagtattggttttatcctgtctgaagcagctaacagttaatgtcttgtcacatttcttatttttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACTTCATATGGCAGCTTTGAATGGTCATTTTGATTGCATGCAATTGTTGATT
|||||| || ||||   |  |    ||||||  | | |||| ||  || | |||||   | |||              || ||| || || ||| |||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||| ||||| || ||||||||||| |||||||||
gtatgtgttgtcaatgaatcac--attttat--tatttgaaacaattatctgttaactccatgt--------------ttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACTTCACATGGCAGCATTGAACGGTCACTTAGATTGCATGCAGTTGTTGATT
















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|13420680|gb|AU174770.1|AU174770
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|29682101|gb|CB678376.1|CB678376
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|29645490|gb|CB650497.1|CB650497
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|29673129|gb|CB669404.1|CB669404
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|29632141|gb|CB637150.1|CB637150
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|29641797|gb|CB646804.1|CB646804
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|86877155|gb|CI311450.1|CI311450
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|29628246|gb|CB633257.1|CB633257
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAGATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|29673087|gb|CB669362.1|CB669362
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|29644924|gb|CB649931.1|CB649931
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
EST: gi|29615014|gb|CB620027.1|CB620027
EST:     AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATC                         TGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT
genomic: AATAGTGGGAGCAGTCCTTGTTCTTCTTTGGGACTGAAATTTAATGAATCgtatgtattt ... tttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtctgaagcagctaacagttaatgtcttgtcacatttcttatttttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACTTCATATGGCAGCTTTGAATGGTCATTTTGATTGCATGCAATTGTTGATT
                          tcttgtcacatttctt  CT-rich tract
                                 acatttcttatttttc  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtattttcaaacgagtattggttttatcctgtctgaagcagctaacagttaatgtcttgtcacatttcttatttttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACTTCATATGGCAGCTTTGAATGGTCATTTTGATTGCATGCAATTGTTGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT