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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acataatgttgattagatggatcattatatattttgcaaatgtaagctttcttgcaccctcatgatggtgtagctgactatgcacacctcaatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATACGCATGCTGGTCCTGGTGGTTATCTGCAGTATGTAGTTTATATTGTTACA

Basic information

species Zea mays
transcript GRMZM2G180732_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180732_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g43520.2 (Oryza sativa), 3'ss of exon 2
acataatgttgattagatggatcattatatattt-tgcaaatgtaagctttcttgcaccctcatgatggtgtagctgactat--gcacacctcaatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATACGCATGCTGGTCCTGGTGGTTATCTGCAGTATGTAGTTTATATTGTTACA
 |  | || |  |  |      | | | |   || ||||    |   | |  |     |  |    | || |  |  |  ||  |    |||||| || |||||||||| ||||||||||||||||| || |||||||||||||| ||||| || |||||||| ||||| |||||||| |||||||||||||||||||| || 
-cccagtgct--tctggccagccttgagacccttatgcagccatgcacctaataaagtctgctcagtagtttttcataacatcagggatcctcaaatttgcagGTATGGTGATCTTTATAATGAGAACAACGTGGCTATCAGTGGCATCCACACTCATGCTGGGCCTGGAGGTTATCTTCAGTATGTAGTTTATATTGTCACG
















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|211192374|gb|FL184214.1|FL184214
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|211189959|gb|FL184194.1|FL184194
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|211189960|gb|FL184195.1|FL184195
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|71323344|gb|DR798328.1|DR798328
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|211192371|gb|FL184211.1|FL184211
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGANAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|211192365|gb|FL184205.1|FL184205
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|211192367|gb|FL184207.1|FL184207
EST:     TGCTTGAAAGACTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: TGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|211189962|gb|FL184197.1|FL184197
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|211189967|gb|FL184202.1|FL184202
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|211189964|gb|FL184199.1|FL184199
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|74240745|gb|DT648659.1|DT648659
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
EST: gi|31363574|gb|CD447931.1|CD447931
EST:     ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGGCTTAAAGCAAG                         GTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC
genomic: ATGGCATCACAGCTTGTTACTATAAAGGTGCTTGAAAGACTTAAAGCAAGgtaagagtga ... aatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttcttgcaccctcatgatggtgtagctgactatgcacacctcaatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATACGCATGCTGGTCCTGGTGGTTATCTGCAGTATGTAGTTTATATTGTTACA
                          agctgac  putative branch site (score: 3)
                                           tcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acataatgttgattagatggatcattatatattttgcaaatgtaagctttcttgcaccctcatgatggtgtagctgactatgcacacctcaatttggcagGTATGGAGATCTTTATAATGAGAATAATGTGGCTATCAGTGGAATCCATACGCATGCTGGTCCTGGTGGTTATCTGCAGTATGTAGTTTATATTGTTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG