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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcatgcttcttttataggaagacccctgtaaagtttgtagctcccttgttaaccttgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC

Basic information

species Zea mays
transcript GRMZM2G146786_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 3
gtatttcatgcttc----ttttataggaagacccctgtaaagtttgtagctcccttgttaaccttgt-------tcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC
||||||||||||      |||| |      | |  ||||   |    |    | |||||     |||       | ||||||||||||||| |||||||| || ||||| ||||| |||||||||||||| ||||| |||||||| |||||||| | |||||||||||| |||||||||||
gtatttcatgctctctgtttttttgtatgaatctgtgtaggttcctcattaactttgttttatgtgtcgatgttttttcagCATTGGACAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGC

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 3
---------------------------------gtatttcatgcttcttttataggaagacccctgtaaagtttgtagctcccttgttaa---ccttgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC
                                 || || | |||   |        |  |  | | |  |||||    || || | ||||     |   | | |||| |||||||| |||||| | ||||| || || |||||||||||||| || || |||||||||||||| || ||||  ||||| || ||||||||||||||
gtacagctctttttcccctgcttttgtgtgtctgtgttgcttgcacttcccgcctcac-atgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
-----------------------------------gtatttcatgcttcttttataggaagacccctgtaaagtttgtagctcccttgttaaccttgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC
                                   || || | |||   |    |    |  |  || ||   | | |    || ||   |   |   | | |||| |||||||| |||||| | ||||| || ||||||||||||||||| || || |||||||| ||||| || ||||  ||||| || ||||||||||||||
gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 3'ss of exon 3
----------gtatttcatgcttcttttataggaagaccc-ctgtaaagtttgtagctcccttgttaaccttg---ttctt-cagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC
           | | ||   ||| |||| |     |  |  || |     ||||  |       | |  ||||   |||||  ||| || || ||||| ||||| ||||| |||||||| || |||||||| || ||||||||||| || |||||  | |  |||||||| ||||| ||||||||
gtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtagCTTTAGATAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGC

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G73350.1 (Arabidopsis thaliana), 3'ss of exon 3
----------gtatttcatgcttcttttataggaagaccc-ctgtaaagtttgtagctcccttgttaaccttg---ttctt-cagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC------
           | | ||   ||| |||| |     |  |  || |     ||||  |       | |  ||||   |||||  ||| || || ||||| ||||| ||||| |||||||| || |||||||| || ||||||||||| || |||||  | |  |||||||| ||||| ||||||||      
gtaccaatctctctctctctctttttttgtttttcgttcttcttttgtagttgtgtcatggccataattcttgagtttcttgtagctttagATAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAA

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S402_46V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------gtatttcatgcttcttttataggaagacccctgtaaagt-ttgtagctcccttgttaaccttgttctt--------cagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC
                                                                   | | |  |  || | ||   | |  |     ||| || | |  | |||  | | ||||     ||| |        |||||||||| || ||||||||||||||| | |||||||||||||||||||| || ||||| |||||  | |  || |  |||||||| ||||| || ||   
gtacagctcaaaacgctatttttagcacattgatatcctatgtactgcatgctgatgtttgatgcatgcagtgaagactccattgtgatggcggagtgtgttaattatcattgctgacctcttaatgcaattcatgaaatgcacagCATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCA--

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S88_45V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------------------------------gtatt-tcatgcttcttttatag-gaagacccctgtaaagtttgtagctcccttgttaaccttgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC
                                                                                                     |||| | |||||| |  | |   ||  | | ||||  |  |  ||    | ||| |||      | | |||||||||| |||||||||||||||||| |||| || |||||||||||||| || ||||| |||||  | |  || |  || || ||| | || ||||| ||
gtacagctcaaacaaagtttatatttacggaatcgagcaatggttatatttatagagatgaatttctatagagttgacgttgatgcttgtcatgtggactctattatgatgcttgtcatgtgttgattatcactgttgatatcatattggcattgataa----aatgtgcagCATTGGATAGCGATGATTTGCTTTACTTGAAGGAACAAATGGAAGCTGAGGAGGATGCCGAGCGTTTGCGCCGGCGAACGGAAAAGAGAGCGTTTGCAGC

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|211273251|gb|FL384319.1|FL384319
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211532797|gb|FL373547.1|FL373547
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGTAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211082871|gb|FL417813.1|FL417813
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211536312|gb|FL400261.1|FL400261
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211413441|gb|FL400135.1|FL400135
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211334889|gb|FL419773.1|FL419773
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211385044|gb|FL404090.1|FL404090
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211421419|gb|FL412843.1|FL412843
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|32943201|gb|CF048020.1|CF048020
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211024425|gb|FL373964.1|FL373964
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211527056|gb|FL387984.1|FL387984
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211500127|gb|FL425199.1|FL425199
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211494457|gb|FL428223.1|FL428223
EST:     ATGCMAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCCAATGGAAGCTKAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211346219|gb|FL403635.1|FL403635
EST:     ATGCAAGANGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATNATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|93016518|gb|EB642038.1|EB642038
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211271661|gb|FL410597.1|FL410597
EST:     ATGCAAGAGGTT-CTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|211039375|gb|FL382073.1|FL382073
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAGG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|89758028|gb|DY687371.1|DY687371
EST:     ATGCAAGAGGGTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG
EST: gi|33771049|gb|CF273343.1|CF273343
EST:     ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG                         CATTGGACAGCGATGATTTGCTTTACCTGGAAGAGCAAATGGAAGCTGAAG
genomic: ATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAGgtatttcatg ... tgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttataggaagacccctgtaaagtttgtagctcccttgttaaccttgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC
                                    tgttaac  putative branch site (score: 2)
                                          ccttgttcttc  CT-rich tract
                  taaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcatgcttcttttataggaagacccctgtaaagtttgtagctcccttgttaaccttgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC