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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatttctattgctccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagtattgactggcattttttttcctccatcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGCCCCAAAGGAAATCATGAGGTTGAAGAAGTTAATTGCTTATTGGAAGGAG

Basic information

species Oryza sativa
transcript LOC_Os04g57140.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 21
gtatg-aatttctattgctccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagtattgactggcattttttttcctccatcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGCCCCAAAGGAAATCATGAGGTTGAAGAAGTTAATTGCTTATTGGAAGGAG
  ||| ||  |  |||  |    |||  ||   |   | ||| ||    ||    |   | || |  | | |         | | ||  |||||     | | || |||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||| || || || |||||||||
-catggaaactacattcatatgttatttaa---tgaatatgtgattagtctaaaacgaat-tatattt-tgggacgggaggtagtataatttttgaa--accctgtagGTATGCTTCACGGGTTCGTTGCATTGTTAATGATACGAGCAAGCATGTTGCCCCAAAAGAAATCATGAGGTTGAAGAAGTTGATCGCCTACTGGAAGGAG

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 21
gtatgaatttctattgctccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagta-ttgactggcattttttttcctccatcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGCCCCAAAGGAAATCATGAGGTTGAAGAAGTTAATTGCTTATTGGAAGGAG
    |||| |  |||| |  | ||      | |  | ||   | |     |    || |||     |||  |||   |   |  |||||  |||    |  |||| |||||||||||||| || || |||||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||||| || || || |||||||||
---ggaatctacattgttttaatagtt---tgtagtagtacca-gtataggacattcctgtggtattgtgcagtggctttgtttcatttactttttaac-ccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGCTCCAAAAGAAATCATGAGATTGAAGAAGTTGATCGCCTACTGGAAGGAG
















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|88688275|gb|CI731851.1|CI731851
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88690249|gb|CI734328.1|CI734328
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88691367|gb|CI733950.1|CI733950
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|218496230|gb|FG959153.1|FG959153
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTATCACTGATACGAGCAAGCATGTAGA
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88966705|gb|CI365928.1|CI365928
EST:     ACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGGTCAATGATACGACCAAGCATGTTG
genomic: ACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATT-GTCAATGATACGAGCAAGCATGTTG
EST: gi|88691416|gb|CI733494.1|CI733494
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88688222|gb|CI731798.1|CI731798
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88690034|gb|CI734113.1|CI734113
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88691225|gb|CI735304.1|CI735304
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88688756|gb|CI732332.1|CI732332
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTCGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88690953|gb|CI735032.1|CI735032
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcgtgtacacctgttgagtattgactggcattttttttcctccatcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGCCCCAAAGGAAATCATGAGGTTGAAGAAGTTAATTGCTTATTGGAAGGAG
                     tattgac  putative branch site (score: 2)
                               cattttttttcctcca  putative PPT
                                atttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatttctattgctccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagtattgactggcattttttttcctccatcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGCCCCAAAGGAAATCATGAGGTTGAAGAAGTTAATTGCTTATTGGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG