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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcgtttcactgaggtctagtgtttatgttcatgctcgaacacggttttgtttcccataggaaagctatatcagttcactgagatttgaatgatgtgcagtagtctgatagatttgtctttgtttatgaaagtgatatctatctgatgatctgtgttcgctgttgcttgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTT

Basic information

species Zea mays
transcript GRMZM2G064023_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 15
gtatatcgtttcactgaggtctagtgtttatgttcatgctcgaacacggttttgtttcccataggaaagctatatcagttcactgagatttgaatgatgtgcagtagtctgatagatttgtctttgtttatgaaagtgatatctatctgatgatctgtgttcgctgttgcttgcatt-atagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTT
                                                                           ||    | |||  | | |||||| || | ||  |   |   ||| | ||    | | |  |  | ||  | | |||  | ||    |  ||   | | ||||  |||||||||||||| ||||||||||||||||| |||||||| || ||||||||| ||||||| |||||||||||  ||||| | ||||| |||||||||||||
---------------------------------------------------------------------------caaacaaatgatttct-aatgatctggaataaac-attctctttttgttgaactctaactgaaaaattca-cagatagtatg----ccatgacacattcattcgtagGTTGTTCCTGGCTTTGGTCATGGAGTTCTACGTAAGACCGATCCACGGTATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
gtatatcgtttcactgaggtctagtgtttatgttcatgctcgaacacggttttgtttcccataggaaagctatatcagttcactgagatttgaatgatgtgca-gtagtctgatag-atttgtctttgtttatgaaagtgatatctatctgatgatctgtgttcgctgttgcttgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTT
                                                                                 | ||    |  |||||| ||||   ||| | |    |||| |  |||   |||||      || ||   ||    ||  | || | |    ||   || |||||||||||||| || |||||||||||||| |||||||| || ||||| ||| ||||||| |||||||||||  ||||| | ||||| |||||||||||||
--------------------------------------------------------------------------------tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaattta---gaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
gtatatcgtttcactgaggtctagtgtttatgttcatgctcgaacacggttttgtttcccataggaaagctatatcagttcactgagatttgaatgatgtgcagtagtctgatagatttgtctttgtttatgaaagtgatatctatctgatgatctgtgttcgctgttgcttgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTT
                                                                     |  ||  |  ||||  |  |   | | | ||       |||    ||    | ||||       || |  | || ||||  | || | |    | | |||  ||||     |||||||||||| ||||| ||||||||| ||||||| ||||| ||| | |||   |||||||||||||||||  ||||||| ||||| || |||||||| |
------------------------------------------------------------------tttccctaatatctcacc-atctcatactaacgtttgaacctctttaggagccctttttg-----acaaattgtttccatctc-taatttat---tgttattgtgtgca-----gGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT

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|6020672|gb|AW065480.1|AW065480
EST:     CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGATTTGGCCATGGAGTTCTGCGCAAGACAGACCCACGGTAT
genomic: CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatatcgtt ... tgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
EST: gi|5847106|gb|AW000185.1|AW000185
EST:     TAAAGAGTGGAAAG                         GTTGTTCCTGGATTTGGCCATGGAGTTCTGCGCAAGACAGACCCNCGGTAT
genomic: TAAAGAGTGGAAAGgtatatcgtt ... tgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
EST: gi|67022591|gb|CO451340.1|CO451340
EST:     GATCAACTCAAAGAGTATGTCTGG-ACACACTAAAGAGTGGAAAG                         GTTGTTCCTGGATTTGGTCATGGAGTTCTGCGCAAGACAGACCCACGGTAT
genomic: GATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatatcgtt ... tgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
EST: gi|71450119|gb|DR831169.1|DR831169
EST:     CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
genomic: CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatatcgtt ... tgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
EST: gi|76284364|gb|DV023932.1|DV023932
EST:     CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
genomic: CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatatcgtt ... tgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
EST: gi|6952534|gb|AW424602.1|AW424602
EST:     CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGATTTGGCCATGGAGTTCTGCGCAAGACAGACCCACGGTAT
genomic: CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatatcgtt ... tgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
EST: gi|31361873|gb|CD446230.1|CD446230
EST:     CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGATTTGGCCATGGAGTTCTGCGCAAGACAGACCCACGGTAT
genomic: CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatatcgtt ... tgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
EST: gi|149082724|gb|EE171942.2|EE171942
EST:     GATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
genomic: GATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatatcgtt ... tgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT
EST: gi|5915419|gb|AW053060.1|AW053060
EST:     CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGATTTGGCCATGGAGTTCTGCGCAAGACAGACCCACGGTAT
genomic: CAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatatcgtt ... tgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgaaagtgatatctatctgatgatctgtgttcgctgttgcttgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTT
                  atctgat  putative branch site (score: 4)
            atatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatcgtttcactgaggtctagtgtttatgttcatgctcgaacacggttttgtttcccataggaaagctatatcagttcactgagatttgaatgatgtgcagtagtctgatagatttgtctttgtttatgaaagtgatatctatctgatgatctgtgttcgctgttgcttgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT