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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttgtcatttagataccgtgttcatctaggagtgtctctttggcggattgatgcggtagctcaccagtgcatgtttgtggtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g64219.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g64219.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G035150_T03 (Zea mays), 5'ss of exon 10
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttgtcatttagataccgtgttcatctaggagtgtctctttggcggattgatgcggtagctcaccagtgcatgtttgtggtgcag
|||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||    ||||    |  ||  ||||| || ||    ||| | ||  | |  || ||   || |    |   |||     ||  |     
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatgtcgcc-atttagtgtgttgatgta----tgtttgttgagtgt-ttaatttcgttgtcttctgttgc-----tgcag-----

upper sequence: LOC_Os03g64219.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G035150_T01 (Zea mays), 5'ss of exon 10
---------------------------------------TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttgtcatttagataccgtgttcatctaggagtgtctctttggcggattgatgcggtagctcaccagtgcatgtttgtggtgcag
                                       |||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||    ||||    |  ||  ||||| || ||    ||| | ||  | |  || ||   || |    |   |||     ||  |     
AGGTTTTGGCTATCTAAACTCAGAAGTCCTGTTGTGCAGTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAGgtactagatgtcgcc-atttagtgtgttgatgta----tgtttgttgagtgt-ttaatttcgttgtcttctgttgc-----tgcag-----

upper sequence: LOC_Os03g64219.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G35300.3 (Glycine max), 5'ss of exon 10
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttgtcatttagataccgtgttcatctaggagtgtctctttggcggattgatgcggtagctcaccagtgcatgtttgtggtgcag---------------
| ||||   |||| |||||||| |||||||| |||||||| || ||||||||||||||||   ||| |   ||  |||   | || | ||      |  |         ||| |||   |  | ||||      || |  || | ||                
TGATATTTCTGAGCTTTTGGGCAGAGGTGCATTACAACTCAATTTATCCAGAAGGAGgtaacatttttatcttttataagctcttaaactgtagacggttac------aattaatgtattcccacacccagttttgataatgctccattaaatctcttctact

upper sequence: LOC_Os03g64219.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ31563 (Selaginella moellendorffii), 5'ss of exon 8
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttgtcatttagataccgtgttcatctaggagtgtctctttggcggattgatgcggtagctcaccagtgcatgtttgtggtgcag
| |||| ||| || ||||||||||| ||||||||||||||  | ||||| |||||||||| |||||     | | | || |   |   ||   |    || | | || |                                       
TCATATTCTTAAGCTTTTGGGCTGAAGTGCACTACAACTCCGTGTATCCGGAAGGAGgtatagttt---tgtgaaacactggtatgtgctctcaaccactgtgtcgcag---------------------------------------

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|88489736|gb|CI427008.1|CI427008
EST:     CTGAGGTGCAATACAANTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|88475411|gb|CI412682.1|CI412682
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|88489389|gb|CI426661.1|CI426661
EST:     TTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: TTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|88284862|gb|CI406308.1|CI406308
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|29671297|gb|CB667572.1|CB667572
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|88519032|gb|CI446686.1|CI446686
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|88840178|gb|CI079632.1|CI079632
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|88281896|gb|CI403292.1|CI403292
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|33681506|gb|CF309745.1|CF309745
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|88842564|gb|CI081820.1|CI081820
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|86418296|gb|CI032505.1|CI032505
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|88514108|gb|CI441614.1|CI441614
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
EST: gi|88840177|gb|CI079631.1|CI079631
EST:     CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG                         AGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA
genomic: CTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttg ... tgtggtgcagAGTTACCAGTTATGGAGAACAAAAGGAAAAGGTGGTGGCATTTTTAGATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAGgtacagtttgtcatttagataccgtgttcatctaggagtgtctctttggcggattgatgcggtagctcaccagtgcatgtttgtggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG