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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtcaatttgaattttcagggagaaaataattacaaacttctctgaactagatttgcacaacagtattcttatgttagcatttttcttatttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG

Basic information

species Zea mays
transcript GRMZM2G131577_T02
intron # 3
splice site 3'
intron type U2

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|78085080|gb|DV513473.1|DV513473
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|211115551|gb|FL427475.1|FL427475
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|18384847|gb|BM418046.1|BM418046
EST:     CATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG
genomic: CATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|18175340|gb|BM350693.1|BM350693
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|60400816|gb|DN233623.1|DN233623
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|37392111|gb|CF633302.1|CF633302
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|18659819|gb|BM500538.1|BM500538
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|33104417|gb|CF064377.1|CF064377
EST:     GTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATC
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATC
EST: gi|91871711|gb|EB401668.1|EB401668
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|29544321|gb|CB604701.1|CB604701
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|37386069|gb|CF630208.1|CF630208
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTCCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|76924262|gb|DV169881.1|DV169881
EST:     TTCAATTGGTGTTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|86471797|gb|DY238167.1|DY238167
EST:     TTCAATTGGTGTTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGTTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|37386066|gb|CF630206.1|CF630206
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTCCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|18384846|gb|BM418045.1|BM418045
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCGGCCCTGACA
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGGCCCTGACA
EST: gi|22489532|gb|BU049455.1|BU049455
EST:     TTCAA-TGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|211233416|gb|FL467936.1|FL467936
EST:     TTCAATTGGTGYTAATACATGGGKGGTCAGTGGAACTCCMCAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|16920324|gb|BM074598.1|BM074598
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|19436302|gb|BM952712.1|BM952712
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|50332820|gb|CO527946.1|CO527946
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATTTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|18384733|gb|BM417932.1|BM417932
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|67020870|gb|CO449619.1|CO449619
EST:     TTCAATTGGTGCTAATACAT-GTTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|37388804|gb|CF631614.1|CF631614
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|16745989|gb|BM032419.1|BM032419
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|18384732|gb|BM417931.1|BM417931
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|78083088|gb|DV511481.1|DV511481
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
EST: gi|86474995|gb|DY241365.1|DY241365
EST:     TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGA                         AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
genomic: TTCAATTGGTGCTAATACATGGGTGGTCAGTGGAACTCCACAGACAAAGAgtatgttctc ... atttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaactagatttgcacaacagtattcttatgttagcatttttcttatttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG
                                   catttttcttattt  CT-rich tract
                                    atttttcttatttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtcaatttgaattttcagggagaaaataattacaaacttctctgaactagatttgcacaacagtattcttatgttagcatttttcttatttgaacagAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC