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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAAGGATGGGCATAAGAGAGATTTTGGTTTTGTTCACTTTGCTGAAAGATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgttttctccttgtttatcatttatcattatttatggaacttggtattctttgtttaggtagttgcttcctgtggaaagcagatatgtttagatca...

Basic information

species Oryza sativa
transcript LOC_Os11g14430.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g14430.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G103430_T04 (Zea mays), 5'ss of exon 6
GCTAAGGATGGGCATAAGAGAGATTTTGGTTTTGTTCACTTTGCTGAAAGATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgttttctccttgtttatcatttatcattatttatggaacttggtatt-ctttgtttaggtagttg---cttcctgtggaaagcagatatgtttagatca
|| |||| ||| ||||||||||| ||||| |||||||||||||| ||||||||||||||| ||||||||||||||||||| |||||||||||| |  |||||||  || ||| | || | |||||  |   ||   | || || |  |     |  |        | |      ||  | | |||   |  |||    | || |
GCCAAGGCTGGTCATAAGAGAGACTTTGGCTTTGTTCACTTTGCAGAAAGATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttctctacctgct-atcatcca--gtttcctgtgaaattcagagccacagtagcagcacaatcagaatttgtttttgaacaaaattat-cagaaatta

upper sequence: LOC_Os11g14430.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G00830.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTAAGGATGGGCATAAGA-GAGATTTTGGTTTTGTTCACTTTGCTGAAAGATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgttttctccttgttta--------tcatttatcattat-----ttatggaacttggtattctttgtttaggta-gttgcttcctgtggaaagcagatat-gtttagatca-----------------------
 |   | | |||   || | | |||||||| ||||| |||| |||||||||||| |||||| ||||||| || ||||  | ||| | ||||||| | ||||||||  |||| |  |  | ||          ||| |  |||||     |||||  |     |  ||| |  |   ||| |||  ||| | |  | ||  | ||| |  ||   ||                       
-CCTGGAAAGGGTGGAAAACGTGATTTTGGGTTTGTCCACTATGCTGAAAGATCTAGTGCATTGAAGGCTGTCAAAGATACCGAGAGATATGAAGTCAATGgtaagtttttttagtcatctagaagacagctattgagtattatgaacgttatgctatcaatttgtctctaatggcgtatgttttttcgtctcaagagatgttattgagtaacacattccacaaacttgcaaactacag
















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|218503841|gb|FG957229.1|FG957229
EST:     ATTAAGTGCACTGAAGGCAGTTAAAGGAAGTGAAAAATATGAATTCGATG                         GGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
genomic: ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgtttt ... tgaaacacagGGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
EST: gi|29639969|gb|CB644978.1|CB644978
EST:     ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATG                         GGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
genomic: ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgtttt ... tgaaacacagGGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
EST: gi|88394072|gb|CI684740.1|CI684740
EST:     ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATG                         GGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
genomic: ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgtttt ... tgaaacacagGGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
EST: gi|218479912|gb|FG956819.1|FG956819
EST:     ATCAAGTGCACTGAAGGCAGTTAAAGGAAGTGAAAAATATGAATTCGATG                         GGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
genomic: ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgtttt ... tgaaacacagGGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
EST: gi|88326998|gb|CI676114.1|CI676114
EST:     ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATG                         GGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
genomic: ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgtttt ... tgaaacacagGGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
EST: gi|88577946|gb|CI674563.1|CI674563
EST:     ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATG                         GGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
genomic: ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgtttt ... tgaaacacagGGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
EST: gi|29640012|gb|CB645021.1|CB645021
EST:     ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATG                         GGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
genomic: ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgtttt ... tgaaacacagGGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
EST: gi|38473107|gb|CF957239.1|CF957239
EST:     ATCAAGTGCACTGAAGGCAGTTAAAGGAAGTGAAAAATATGAATTCGATG                         GGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG
genomic: ATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgtttt ... tgaaacacagGGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAAGGATGGGCATAAGAGAGATTTTGGTTTTGTTCACTTTGCTGAAAGATCAAGTGCACTGAAGGCAGTTAAAGGAAGCGAAAAATATGAATTTAATGgtaatgttttctccttgtttatcatttatcattatttatggaacttggtattctttgtttaggtagttgcttcctgtggaaagcagatatgtttagatca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA