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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctctctctcccctccaccccctctccctgtgataacatttccttttttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG

Basic information

species Zea mays
transcript GRMZM2G079538_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 5
------gtatgctctctctctcccctccaccccctc--------tccctgtgataacattt--cctttttttta-acagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG
       |   ||||||||||| |   ||| | | |        | | | || | ||| ||  ||||  ||| | ||||||||||| |||||||| ||||||||||| || ||||| ||||||||||||||||||
gtatgatttctctctctctctctctctcacacacacacatcaggttcatttgcttacaattaaccttcctttaatacagAACCTGGTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG

upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 2
----------------gtatgctctctctctcccctccaccccc-----tctccctgtgataacatttccttttttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG
                 |||  | ||    ||      |   |      | |  ||   |    |||| ||      |  |||||||||| || |||||| ||||||||||  |||| || || |||||||||||||||
gtatgtctcttttgcattatcttttccggttctttctgatgtctgaatatatatctaaaagttaatttgctggcacatttcagAACCTGGTGAGAGAGTCCAGGCTGATGAGGCTATTGCACAAATTGAAACTGATAAG
















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|211233033|gb|FK998526.1|FK998526
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGA
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGA
EST: gi|78103875|gb|DV522298.1|DV522298
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|211169881|gb|FL077610.1|FL077610
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|148950981|gb|EC896624.2|EC896624
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|31355469|gb|CD439826.1|CD439826
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|5343075|gb|AI795485.1|AI795485
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|31355590|gb|CD439947.1|CD439947
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|148978727|gb|EE026283.2|EE026283
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|211321201|gb|FL380429.1|FL380429
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAGAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|211169879|gb|FL077608.1|FL077608
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|148958216|gb|EC904424.2|EC904424
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|31358640|gb|CD442997.1|CD442997
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|211325989|gb|FL407943.1|FL407943
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|148991485|gb|EE033000.2|EE033000
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|149014456|gb|EE044070.2|EE044070
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|149003557|gb|EE038930.2|EE038930
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|67033243|gb|CO461992.1|CO461992
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|148943959|gb|EC889039.2|EC889039
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|211169872|gb|FL077601.1|FL077601
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGANGGCTGATGAACCTATAGCGCAGATTGAAACT
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGA-GGCTGATGAACCTATAGCGCAGATTGAAACT
EST: gi|148931436|gb|EC874404.2|EC874404
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|149081048|gb|EE170148.2|EE170148
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|149015063|gb|EE044815.2|EE044815
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|211169620|gb|FL396011.1|FL396011
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAAACT
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAA-CT
EST: gi|31353408|gb|CD437765.1|CD437765
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|29576970|gb|CB617082.1|CB617082
EST:     ACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
genomic: ACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTG
EST: gi|211233034|gb|FK998527.1|FK998527
EST:     CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA                         AAC-TGGGAGACAGA
genomic: CTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGAgtatgctctc ... tttttaacagAACCTGG-AGACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctctcccctccaccccctctccctgtgataacatttccttttttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG
                             tgataac  putative branch site (score: 2)
                                   catttcctttttttt  CT-rich tract
                               ataacatttccttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctctctctcccctccaccccctctccctgtgataacatttccttttttttaacagAACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT