Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagtgaattctttgagcttcaaaggatattgataaccttttgacagtttgatgtttccttgttaatactctaacctgatcatgatgacatttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 14
tttagtgaattctttgagcttcaaaggatattgataaccttttg--acagtttgatgttt--ccttgtt--aatactc--taacctgatcatgatgacatttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG
      | || ||  |      | |  || |  |||||   | |  |  | |||||  |   | | |||  |||  |   || | |  || |  |    ||||| ||||||||||| |||||  |||||||  ||||||| ||||||||||| ||||||||  |||||||||| |||||||||||||| ||||||||| ||
----cagcatcctacgga----acaatatgtgaataactgatggttatggcttgatcctcagcatggttgtaatgttgcatatctttctcttttttttttttttgcagAGACCAGAAAAGTACTTAGGTGATATTGAAACCTGGAACAAAGCAGAGCAACAGCTGACAGAAGCCTTAAATGAGTTTGGAAAGCCATGGCAG
















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|211046688|gb|FL336954.1|FL336954
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|32832908|gb|CD972586.1|CD972586
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|67033102|gb|CO461851.1|CO461851
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|22545540|gb|BU097899.1|BU097899
EST:     ATGTTTATGAGAATATTTGGGTTTAAAAAATGGAGTGGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATGTTTATGAG-ATATTT-GGCTTCAAATAT-GAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|211181488|gb|FL345837.1|FL345837
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|32934180|gb|CF038992.1|CF038992
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGCTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|32832310|gb|CD971988.1|CD971988
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|211197538|gb|FL314132.1|FL314132
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|32834031|gb|CD973709.1|CD973709
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|50324858|gb|CO519984.1|CO519984
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA
EST: gi|32835314|gb|CD974992.1|CD974992
EST:     ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG                         AGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAACAA
genomic: ATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 296

ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 217

ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 230

ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACGgtattcttct ... atttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttgatgtttccttgttaatactctaacctgatcatgatgacatttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG
                                            catttttcc  CT-rich tract
               ttgttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagtgaattctttgagcttcaaaggatattgataaccttttgacagtttgatgtttccttgttaatactctaacctgatcatgatgacatttttccagAGACCAGAGAAGTATCTAGGTGAAGTTGAAACTTGGAACAAAGCTGAGCAACAATTGACAGAAGCTTTAAATGAGTTTGGGAAGCCATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - agcttca
- - - - - - - - - - - - - - - - - - - - - - - - tttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatga