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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttccataatatcctagatagtgataacttgtagtaactaacttctgaacaagtccatatatgtctcaatcaaaaactttatatgacacttttgatagGGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTG

Basic information

species Oryza sativa
transcript LOC_Os11g03780.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G30470.1 (Glycine max), 3'ss of exon 6
--gatttccataatatcctagatagtgat--aacttgtagtaactaacttctgaacaagtccatatatgtctcaatcaaaaactttatatgacacttttgatagGGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTG
  ||| |   |  | ||| |  |  |  |  || ||||  |    || |  |||| |  | || |||  |   ||    ||     || |    |||   | ||| || || ||| |||||||  |    ||||||||||| ||  ||||||  || |   |||| ||||||||||||||||||||||||||||| ||||||||
atgatctatctcttttccaatttcttcctctaatttgtctt---caagtcatgaa-acattcaaataacttcaaaatttaacgcaaatttttatcttgcaagagGTGGCTGTTTTATTGAAGGACAAACATTAAGAAATGCATTTCGGTGGAAAGATAGAGTTGGACCCTGGGAACAGAGACCTGGGCACTTTGGTGATGTTTG

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 6
gatttccataatatcctagatagtgataacttgtagtaactaacttctgaacaag--tccatatatgtctcaa-tcaaaaactttatatgacacttttgatagGGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTG
    |||||  | |     ||  |  |  || | | |        | | | ||||  | || |||  |  ||| |  ||  |  | | | |  ||||  | ||| || || |||||||||||  |    ||||||||||| ||  ||||||  || | | |||| ||||||||| |||||||||| |||||||| ||||||||
atgatccatcttttttccaat--ttcttcctcgaatttgtctttatgtcatcaagcgttcaaataacttccaaatttaatgcaattttttat-ctttcaagagGTGGCTGTTTTGTTGAAGGACAAACATTAAGAAATGCATTTCGGTGGAAAGATAGTGTTGGACCCTGGGAAGAGAGACCTGGTCACTTTGGTGATGTTTG
















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|33796127|gb|CF323929.1|CF323929
EST:     ACTACTATACATGCTTTTGGAATTAAAACCACAGTTCCTACGCTTTC-TG                         GGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGG
genomic: ACTACTATACATGCTTTTGGAATTAAAACCACAGTTCCTACGCTTTCCTGgtatttcttg ... cttttgatagGGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGG
EST: gi|33796277|gb|CF324005.1|CF324005
EST:     ACTACTATACATGCTTTTGGAATTAAAACCACAGTTCCTACGCTTTCCTG                         GGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGG
genomic: ACTACTATACATGCTTTTGGAATTAAAACCACAGTTCCTACGCTTTCCTGgtatttcttg ... cttttgatagGGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGG
EST: gi|88722894|gb|CI746404.1|CI746404
EST:     ACTACTATACATGCTTTTGGAATTAAAACCACAGTTCCTACGCTTTCCTG                         GGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGG
genomic: ACTACTATACATGCTTTTGGAATTAAAACCACAGTTCCTACGCTTTCCTGgtatttcttg ... cttttgatagGGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaacaagtccatatatgtctcaatcaaaaactttatatgacacttttgatagGGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTG
                                           cactttt  CT-rich tract
                        aatcaaaaactttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttccataatatcctagatagtgataacttgtagtaactaacttctgaacaagtccatatatgtctcaatcaaaaactttatatgacacttttgatagGGGGGTGCTTTGTTGAAGGCGATTGGTTAAGAAATGCTTTCAGGTGGAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG