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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

Basic information

species Zea mays
transcript GRMZM2G165357_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 7
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
|||  | ||||| | | | || |  | |  ||||    |   ||||| |||  ||  |   |||||| |||||    || | || | ||  ||   |||||| || |||||||| ||||| |||||||||||||| ||||| || |||||||| |||||||||||||||||||||||||
gtacgtctgttc-tatcacaaatacactacatttatcctatattttcttaatctag-tgcaaagttcacttac----ttgaattgatttacttc--atcagGAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttac----aatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
  ||   |  ||  ||  ||  |  |  |||| ||   |  ||| |||| |  | |   |    | || |||     |   |  |  |||   | | |  | |||| ||| ||||||||||||||||||| |||||||| ||||| ||  ||||||| || ||||| |||||||| || || |
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgca-cagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
-gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttct-atcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
    ||||||      |||  || ||  || || |        |  | ||   ||    |     ||     | |   |  |  |||   | | | | | |||| ||| ||||||||||||||||||| |||||||| ||||| ||  ||||||| || ||||| ||||||||||| || |
taggaatttg---gaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaattttt--atttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
               |   | |  | | ||||  |||||   || ||  || ||||||  |  ||    | ||| | ||   | ||   || | || |   |||||||||||| ||||||||||| || |||||||| || |||||  ||||||| ||||| |||||||| ||||| ||||
--------------gtaggagtaaacacttatcagcttttaattctc--aacttatctg-cgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 7
--gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
  | | | |      | ||     |    |   |||   | ||      | | |   | | || |  | |  | | || |   ||    | | | | |  |||| || |||||||| ||||||||||| ||||| || || || || |||||||| || ||||||||||||||||| || |
tagcagactgacatttttggcggctctgttaattttatgtaggaaa---aaagaccttttctctaactatgattctatatgccttccgttatatatattacagGAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ17446 (Selaginella moellendorffii), 3'ss of exon 6
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
                                       |    | ||  |  ||| | ||   || |||   | |   |  | |   || |  | | ||||||||||||| || || || ||||| || || || || || ||| ||||||| ||||||||||||||||| || ||||
---------------------------------------gtacgtgcaccagatatttgtc---ttgtct---actgcctgctca---ttgtgccgagcagGTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ35029 (Selaginella moellendorffii), 3'ss of exon 6
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
                                       |    | ||  |  ||| | ||   || |||   | |   |  | |   || | || | ||||||||||||| || || || ||||| || || || || || ||| ||||||| ||||||||||||||||| || ||||
---------------------------------------gtacgtgcaccagatatttgtc---ttgtct---actgcctgctca---ttgtgtcaagcagGTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG

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|149070503|gb|EE158907.2|EE158907
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGGTA-GCGTGTAGCAGAGACGCTGATG
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGG-TAAGCGTGTAGCAGAGACGCTGATG
EST: gi|32838870|gb|CD978551.1|CD978551
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|32850602|gb|CD990283.1|CD990283
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
EST: gi|15100352|gb|BI396143.1|BI396143
EST:     ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG                         GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT
genomic: ACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTGgtaaatttgt ... tttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
                                  atttaac  putative branch site (score: 3)
                             tttttatttaactttt  CT-rich tract
                  ttctcttacaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT