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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattttttatattcacagagattattagctttgatatgtcatatcaccttttttgttgagtcctaggaaatttttgtctgaatgacatttcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAGATTAAGGAGATTTTTGAAAAGCATGGAGAGGTCACAAAAGTCGTTTTGC

Basic information

species Oryza sativa
transcript LOC_Os11g14430.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 5
----caattttttatattca-cagagattattagctttgatatgtcata--tcaccttttttgttgagtcctaggaaatttttgtctgaatgacatttcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAGATTAAGGAGATTTTTGAAAAGCATGGAGAGGTCACAAAAGTCGTTTTGC
       || |||| |   | |   | || | |  |||  ||||    |  |  |||| | |||||| |    |   ||||   | |     ||| || ||   ||||||||||||||||||||||||||| |||| ||||||| ||||||||||||||| |||||  | ||||| || |||||||||||||||||| ||||| |||
atcctgtttctttagagcaatctttgcttctaaatttttgtatgcagaaattgcccttctctgttgact----gaggatttgaatatttgctacaattact---cagGTGAAGACTATATATGTGAAGAACCTACCTGAAAATGTTTCTAAAGAGAAGATAAAGGACCTGTTTGACAAACATGGAGAGGTCACAAAAATCGTTCTGC
















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:     GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
EST: gi|29639969|gb|CB644978.1|CB644978
EST:     GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
EST: gi|88394072|gb|CI684740.1|CI684740
EST:     TTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: TTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
EST: gi|218479912|gb|FG956819.1|FG956819
EST:     GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
EST: gi|29664577|gb|CB660852.1|CB660852
EST:     GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
EST: gi|88326998|gb|CI676114.1|CI676114
EST:     TTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: TTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
EST: gi|58609361|gb|CK037394.1|CK037394
EST:     GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
EST: gi|58693279|gb|CK081966.1|CK081966
EST:     GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAA
genomic: GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAA
EST: gi|88577946|gb|CI674563.1|CI674563
EST:     TTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: TTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
EST: gi|29640012|gb|CB645021.1|CB645021
EST:     GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
EST: gi|38473107|gb|CF957239.1|CF957239
EST:     GCTGGGCTGAACCTTTTGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAG                         GTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG
genomic: GCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatctttac ... tcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccttttttgttgagtcctaggaaatttttgtctgaatgacatttcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAGATTAAGGAGATTTTTGAAAAGCATGGAGAGGTCACAAAAGTCGTTTTGC
                                         catttccttt  CT-rich tract
                       aaatttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattttttatattcacagagattattagctttgatatgtcatatcaccttttttgttgagtcctaggaaatttttgtctgaatgacatttcctttacagGTGAAGACTATATATGTGAAGAACTTACCAGAAAATGCTTCTAAAGAGAAGATTAAGGAGATTTTTGAAAAGCATGGAGAGGTCACAAAAGTCGTTTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG