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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaactgagggagtaccttccagcccttagtcaaacagctaggggaatcaaattatccttctccgatttactgacagaatccacctactgcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTGCCTCCAAAGCGTGGGATCACACAATACCACCCGATCCATTAGAGAGCAG

Basic information

species Zea mays
transcript GRMZM2G174286_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 10
tggaactgagggagtaccttccagcccttagtcaaacagctaggggaatcaaat-tatccttctccgatttactgacagaatccacctactgcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTGCCTCCAAAGCGTGGGATCACACAATACCACCCGATCCATTAGAG-AGCAG
   ||   |   |   | | |||     |||    | |  ||    |   |  | | | ||  ||  || |||| ||| ||| | |  | |      ||||||||||||||| || ||||||||| ||||||| ||||| ||| |||||||||| || || || |||||||||||||| || || || |||||||| |||  
-aaaagaaaaataaatcataccacgggatagctccagaagtatcatatatatttgtttactgttcttatatactaacaaaattctctaatttttttggcagCTGGTTGAGATCGTACCTTCAGCTTTGGTGCTATTCATCCTAAGGAAACTGCCACCGAAACGGGGGATCACACAATATCATCCAATTCATTAGAGCAGCC-

upper sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 11
lower sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 10
tggaactgagggagtaccttccagcccttagtcaaacagctaggggaatcaaattatccttctccgatttactgacagaatccaccta---ctgcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTGCCTCCAAAGCGTGGGATCACACAATACCACCCGATCCATTAGAGAGCAG-
|  ||    |    |  | |  ||    |  | | |  | ||   |  |    || ||||| |    ||| |        |   | |    || |   | ||| |||| |||||| |||||||| ||||||| || |||||| |  ||||  |||||||||||||||| ||||||||||| || || || |  || |||| |  
tataatcttgt---tttcatatagtttctcttaatattgttacttgttttcttttttccttatttcctttgccttttttttgtgcttttgcctacctttacagTTGGTGGAGATACTGCCTTCATCTCTGGTCCTTTTCATTTTGAGGAAGTTGCCTCCAAAGCGTGGTATCACACAATATCATCCTATTCGCTA-AGAGGATT
















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|18170253|gb|BM340093.1|BM340093
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTGTTGTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTC-ACAGGAAACT
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTAC-GGAAACT
EST: gi|93284395|gb|EB676659.1|EB676659
EST:     CAGATCTTGATGTTTTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|149112907|gb|EE295706.2|EE295706
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|88754539|gb|DY538680.1|DY538680
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTTTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|5922262|gb|AW055551.1|AW055551
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|24765679|gb|CA400838.1|CA400838
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|32827198|gb|CD966876.1|CD966876
EST:     GATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: GATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|71300276|gb|DR786208.1|DR786208
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|28985354|gb|CB350599.1|CB350599
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|88749638|gb|DY533779.1|DY533779
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|78106688|gb|DV525106.1|DV525106
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|5739982|gb|AI947672.1|AI947672
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|6095420|gb|AW120087.1|AW120087
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|45846980|gb|CN070923.1|CN070923
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|101383586|gb|EB813848.1|EB813848
EST:     CAGATCTTGATGTTTTGAACCATCCAATCCTGAACTTTTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|18174253|gb|BM349641.1|BM349641
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|67017793|gb|CO446542.1|CO446542
EST:     CAGATCTTGATGTTCTGAACCATCCA-TCCTGGACTTCT-CTATTACCTG                         CTGGNTGAGATAGT
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGT
EST: gi|67020535|gb|CO449284.1|CO449284
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|113671235|gb|DW821941.1|DW821941
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTNAGCTCTGGTGCTCTTC
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTC
EST: gi|211179297|gb|FL465342.1|FL465342
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|37383767|gb|CF628916.1|CF628916
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|211215684|gb|FL434860.1|FL434860
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|31364203|gb|CD448558.1|CD448558
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
EST: gi|5757367|gb|AI964654.1|AI964654
EST:     CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG                         CTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG
genomic: CAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTGgtatgaattt ... gcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcaaattatccttctccgatttactgacagaatccacctactgcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTGCCTCCAAAGCGTGGGATCACACAATACCACCCGATCCATTAGAGAGCAG
                        tactgac  putative branch site (score: 1)
     aaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaactgagggagtaccttccagcccttagtcaaacagctaggggaatcaaattatccttctccgatttactgacagaatccacctactgcgactgcagCTGGTTGAGATAGTGCCTTCAGCTCTGGTGCTCTTCATTCTACGGAAACTGCCTCCAAAGCGTGGGATCACACAATACCACCCGATCCATTAGAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG