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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttagggaaaaaatcctgtcaagctgaagaaaccccgtattttattaccagtctgtaggctatagattaacgtaaatttctgcttgccttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG

Basic information

species Zea mays
transcript GRMZM2G452529_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G452529_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 10
-ttgttagggaaaaaatcctgtcaagctgaagaaaccccgtattttattaccagtctgtaggctatagattaacgtaaatttctgcttgccttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG
 || ||  ||  |  ||   | || ||   |  |          |  | || ||  |  | | |  |  ||     |  | |     | | |||||||||||||||||||||||| |||||||||||||| ||||||||||||||  | || || |||| |||||||||| |||||||||| |||
tttattctggtcagtatta-gacatgcatgattattttttatcatcctaacaagctttcatgttgcaagttgctaaacttgttcctgttcattttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG

upper sequence: GRMZM2G452529_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G32660.1 (Glycine max), 3'ss of exon 9
ttgttagggaaaaaatcctgtcaagctgaagaaaccccgtattttattaccagtctgtaggctatagattaacgtaaattt---ctgcttgccttt-tccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG
||      |   |      | |  |  |   |||||    ||  || ||||   || |    ||||  |  |   |||| |   |   |||||||  |    ||||||||||||| ||||||||||||||||| || || |||||  |||  || || |   |||| ||||| || || ||||| |||
tttcatttgttgaggctaggactggaagtcaaaacc----atactagtacccagctttgatgtataagtcgagcaaaatctgaccaatttgccttggtgtgtagATGGTTATGGCCGTGTTTGCATACATATATCATCAGTCATTTGTTGTGCCGCAAACTCTCTCGGTTGAAATGATTTTGGACCAG

upper sequence: GRMZM2G452529_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 10
ttgttagggaaaaaatcctgtcaagctgaagaaaccccgtattttattac-cagtctgtaggctatagattaacgtaaatt--tctgcttgccttt-tccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG
      || ||    |  | |  |         ||    |   | | ||| |  | ||||  || ||| | | |  || ||   |   ||| |||  |    ||||||||||||| ||||||||||| ||||| || ||||||||  |||  || || |   |||| ||||| || || ||||| |||
---actggcaactcctatttttcactctcctttacattctgcctcagtacactatttgtat-ctttagttgagcaaaatttgaccaatttgtcttggtgtgtagATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCGCAAACTCTCTCAGTTGAAATGATTTTGGACCAG

upper sequence: GRMZM2G452529_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 10
---------------------------------------------ttgttagggaaaaaatcctg-----tcaagctgaagaaaccccgtattttattaccagtctgtaggctatagattaacgtaaatttctgcttgccttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG
                                             |  |||| |     || |       ||    || | |  |  | | | | | |  ||   |  ||  |||| || |||   |  |  || |  |  ||    ||||||||||||||||| ||||| |||||||| |  |||||||| ||||   | || | | | || ||||| | |||| | || |||
gtaactctaatgaaactagtatctcttcgtaagattatgattaggtctttagagttttcattcacaagattcgcattgcatattcttcttctctaactctcatctttaagcatatacataaaccagacctaatgttatctattgttacagATGGTTATGGCAGTATTTGCCTACATATATCTTCAATCATTTATTGTCTCCCAAAGCGTTTCGGTTGACAAAATCCTAGACCAG

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|5871566|gb|AW018037.1|AW018037
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
EST: gi|166616965|gb|EG156756.1|EG156756
EST:     AGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCA
genomic: AGCATACCTGGGCATGGTGGAATTACTGACAGAATGGA-TTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCA
EST: gi|4646646|gb|AI491480.2|AI491480
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTG
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTG
EST: gi|88753935|gb|DY538076.1|DY538076
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
EST: gi|71761916|gb|DR959853.1|DR959853
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
EST: gi|211372465|gb|FL432864.1|FL432864
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
EST: gi|7145231|gb|AW506712.1|AW506712
EST:     CTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
genomic: CTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
EST: gi|6031444|gb|AW076346.1|AW076346
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
EST: gi|78021196|gb|DV489583.1|DV489583
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
EST: gi|5915325|gb|AW052966.1|AW052966
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATNCATATACCCCCAATCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
EST: gi|78023335|gb|DV491722.1|DV491722
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaccagtctgtaggctatagattaacgtaaatttctgcttgccttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG
                     gattaac  putative branch site (score: 2)
                                 tttctgcttgcctttt  putative PPT
                      attaacgtaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttagggaaaaaatcctgtcaagctgaagaaaccccgtattttattaccagtctgtaggctatagattaacgtaaatttctgcttgccttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG

- - - - -aaaaaat
- - - - - - - - - - - - gctgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtaggc