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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgttttcatacccaccttcctttatatctgtatatgtactgcatgactgaaatttgtttctcaacacaagagggattatttacgatgctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG

Basic information

species Zea mays
transcript GRMZM2G168629_T01
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T04 (Zea mays), 3'ss of exon 26
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 26
--acttgttttcatacccaccttcctttatatctgtatatgtactgcatgactgaaatttgtttctcaacacaagagggattatttacgatgctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG
  | |  ||||   ||     ||| | | |   ||| ||||    | || ||  |   |    |  |  |      |   |  | |   |  |  | || ||| ||||| || || ||||||||||||||| ||||||| |||||||||||||||||||||||||| || || || || |
gcagtgcttttttcactagtattcgtatcttcttgtttatgcttagtat-acacacgctgtaataactgcttttttgttgtcttatggaac-cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG

upper sequence: GRMZM2G168629_T04 (Zea mays), 3'ss of exon 26
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 27
-------------------------------------------------------------------------------------acttgttttcatacccaccttcctttatatctgtatatgtactgcatgactgaaattt-gtttctcaacacaagagggattatttacgatgctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG
                                                                                       ||  ||||||  |  |  | ||  |  |   |  ||||  |  ||   |||| ||| |||| |||   |  ||      ||| |    ||| |   |||| ||||| || || ||||||||||||||| | || || ||||| || |||||||||||||| ||||||||  | || |
gtgcgtttttatttttttatttttaacaagaccatcattcttttttacttcactttatttttttcacccttttccccccactttagtttagtttcatttcagc--tgctaaaagttatttcatgt-ttctatacttgaagtttagtttatcacttcctgaactgaaattgatttggctcttctcagATCATTATGATGTCAAAATGCCTTGCCATCTTATCCTTTCAAAACTTGCAGACAAGTGCCCATCCGCCGTATTGGCAG

upper sequence: GRMZM2G168629_T04 (Zea mays), 3'ss of exon 26
lower sequence: PP1S35_209V6.1 (Physcomitrella patens), 3'ss of exon 26
---acttgttttcatacccaccttcctttatatctgtatatgtactgcatgactgaaatttgtttctcaacacaagagggattatttacgatgctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG
    |        ||   ||  ||  || | || ||| |  |   |  ||  ||    | |  |  |||  ||||   |       | |  | |||| |||||| |||||||| ||||||||||| || ||| | || ||||||||| | |||| |||||||      || || || ||||
ggatcaaagcagtatgtgcagttttattaacat-tgtttgaggtttctatt-ctattctattctattcagaacaaaccgtcaccactgct-tcctttgtgcagATCATTACGATGTGAAAATGCCATGTCATCTAATCCTATCAAAGTTGGCAGCCAAGTGCGGAGGTGCAGTTCTAGCTG

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|71430729|gb|DR811779.1|DR811779
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|32924248|gb|CF029060.1|CF029060
EST:     ACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: ACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|71430730|gb|DR811780.1|DR811780
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|5058666|gb|AI737142.1|AI737142
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|32907845|gb|CF012658.1|CF012658
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|18170739|gb|BM340579.1|BM340579
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|4967010|gb|AI691788.1|AI691788
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|211106237|gb|FL467711.1|FL467711
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|166643623|gb|EG090562.1|EG090562
EST:     GTGAATCCATCGTCCTTCTATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTAT
genomic: GTGAATCCATCGTCCTTC-ATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTAT
EST: gi|78119496|gb|DV537880.1|DV537880
EST:     CTTTCCTCTTGTCTGGTTTAGGGG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: CTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|166698756|gb|EG168762.1|EG168762
EST:     GTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGC
genomic: GTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGC
EST: gi|29544507|gb|CB604887.1|CB604887
EST:     AG-GAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGGTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|32924416|gb|CF029228.1|CF029228
EST:     TACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: TACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|120479953|gb|EH210674.1|EH210674
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|24769168|gb|CA404297.1|CA404297
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|32923836|gb|CF028648.1|CF028648
EST:     ACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: ACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|4804473|gb|AI665343.2|AI665343
EST:     AGTGAATCCATCGTCNTTCATTGTACCTTTCNTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|211405020|gb|FL469632.1|FL469632
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|40335220|gb|CK369290.1|CK369290
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|78543741|gb|DV621239.1|DV621239
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|32923972|gb|CF028784.1|CF028784
EST:     ACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTGGCAG
genomic: ACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|113703700|gb|EE681204.1|EE681204
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|50322915|gb|CO518041.1|CO518041
EST:     AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: AGTGAATCCATCGTCCTTCATTGTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|33095774|gb|CF055768.1|CF055768
EST:     ACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: ACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
EST: gi|32923875|gb|CF028687.1|CF028687
EST:     GTACCTTTCCTCTTGTCTGGTTTAGGTG                         ACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG
genomic: GTACCTTTCCTCTTGTCTGGTTTAGGTGgtaagtacgg ... ctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgactgaaatttgtttctcaacacaagagggattatttacgatgctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG
                                           tgctttct  CT-rich tract
       aaatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgttttcatacccaccttcctttatatctgtatatgtactgcatgactgaaatttgtttctcaacacaagagggattatttacgatgctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG

-cttgttt
- - - - - - - -caccttc
- - - - - - - - - - - - - - - - - atatgta
- - - - - - - - - - - - - - - - - - - - - tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacaa