Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggcttcgccttattttttttgtaaccgtctttcccctgtggggattttgtgcttctattcataactgcacctgaatttcgtttgttttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT

Basic information

species Zea mays
transcript GRMZM2G016296_T06
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016296_T06 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 3
gtgggcttcgccttattttttttgtaaccgtctttcccctgtggggattttgtgctt--ctattcataactgcacctgaatttcgtttgttttttg----gcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT
  | || |  |||| |||| ||| |    |  |      |||  || ||| || ||    |  | || | ||   |||| |   |||| ||||  |    ||||| ||| ||||||||||||| |||||||||||||||||||| ||||| || |||||||| ||||||||
--gtgcgtaacctttttttcttttt--ttgattcctttgtgtttgggtttcgttctgaatttctgatgattgagtctga-tggtgttttttttacgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGCCCAATGCGGAGCCAAT
















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|87157632|gb|DY402421.1|DY402421
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|18384287|gb|BM417486.1|BM417486
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|71766439|gb|DR964376.1|DR964376
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|74235570|gb|DT643484.1|DT643484
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|71421374|gb|DR805394.1|DR805394
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211456040|gb|FL150302.1|FL150302
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211422683|gb|FL350037.1|FL350037
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|6022225|gb|AW067153.1|AW067153
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|76280364|gb|DV019932.1|DV019932
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|71317634|gb|DR795571.1|DR795571
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|22489702|gb|BU049625.1|BU049625
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211456031|gb|FL150293.1|FL150293
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|26558961|gb|CA831196.1|CA831196
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|76936777|gb|DV174882.1|DV174882
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|50336916|gb|CO532042.1|CO532042
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|22545919|gb|BU098278.1|BU098278
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|74232258|gb|DT640172.1|DT640172
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211456033|gb|FL150295.1|FL150295
EST:     GCGGTACAAGTACGCCGACGAGGC-CAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211456029|gb|FL150291.1|FL150291
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211456036|gb|FL150298.1|FL150298
EST:     GCGGTWCAAGTACGCCGAMGAGGCGCARAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCARTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|91873269|gb|EB403226.1|EB403226
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211456038|gb|FL150300.1|FL150300
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtgggcttcg ... tttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggattttgtgcttctattcataactgcacctgaatttcgtttgttttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT
                  tcataac  putative branch site (score: 2)
                                   tttcgtttgtttttt  putative PPT
                                        tttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggcttcgccttattttttttgtaaccgtctttcccctgtggggattttgtgcttctattcataactgcacctgaatttcgtttgttttttggcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG