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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggttttggttggtccttttgtggtgtttgtttccagtttatgatggtaccaccttgtgctcttgctgatatgatgatttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAAGCAAAGATCGTAGAAGA

Basic information

species Zea mays
transcript GRMZM2G055020_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055020_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G44810.1 (Glycine max), 3'ss of exon 3
---------gtgaggttttggttggtccttttgtggtgttt---gtttccagttta-tgatggtaccaccttgtgctcttgctgatatgatgatttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAAGCAAAGATCGTAGAAGA
          ||   || |   || || || | |  | ||     |||||  |  | | | | |  ||  |     | |   |  | | ||  ||  | ||||| ||||||||| ||||||| || ||||||||||| |||||| |  |||||||| | || |  |||||
ctatcatgaatgtcattgtttgtgatctttctatattattcccaatttcccatcaactaacgctgtca--tcaaaatttatatcctcttatttttggtgcagGGTTATATTGTCCTAAATAGACCATGGGCTTTTGTTCAGTGGCTGGAGAAAGCAGATATTGAGGAAGA
















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|71443354|gb|DR824404.1|DR824404
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|32840194|gb|CD979875.1|CD979875
EST:     GAGATACCCCACCATTGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: GAGATA-CCCACCA-TGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|149075926|gb|EE164487.2|EE164487
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|149094970|gb|EE180558.2|EE180558
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|71446890|gb|DR827940.1|DR827940
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|149110886|gb|EE294384.2|EE294384
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTC
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTC
EST: gi|78120684|gb|DV539068.1|DV539068
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCCTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|88757364|gb|DY541505.1|DY541505
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGA
EST: gi|71440531|gb|DR821581.1|DR821581
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|149077163|gb|EE165824.2|EE165824
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|71769809|gb|DR967746.1|DR967746
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|71763634|gb|DR961571.1|DR961571
EST:     GGCAAGGATCAG                         GGATATATTGTCTAAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: GGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|71428101|gb|DR809151.1|DR809151
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|71449379|gb|DR830429.1|DR830429
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|211218550|gb|FL110185.1|FL110185
EST:     ATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|71439617|gb|DR820667.1|DR820667
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|78082144|gb|DV510556.1|DV510556
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGG
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGG
EST: gi|76015781|gb|DT942951.1|DT942951
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|91048418|gb|EB158836.1|EB158836
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
EST: gi|149103179|gb|EE288550.2|EE288550
EST:     ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAG                         GGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA
genomic: ATGAGATACCCACCATGGTGGTTGATCCCCTTCCTGAAGGCAAGGATCAGgtgaggtttt ... atttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagtttatgatggtaccaccttgtgctcttgctgatatgatgatttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAAGCAAAGATCGTAGAAGA
                                tgctgat  putative branch site (score: 3)
                                              tttatcc  putative PPT
                                     atatgatgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggttttggttggtccttttgtggtgtttgtttccagtttatgatggtaccaccttgtgctcttgctgatatgatgatttatccagGGATATATTGTCTTAAATAGGCCTTGGGCTTTTGTCCAGTGGATCCAGAAAGCAAAGATCGTAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG