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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgagtgagtctaccgctattattcagtctgaatccagtaaatcagaattccacaggataatagtacctatatttcctgcaaagacaaattgtacatacatcaaaagcatctcgcatggcatgttttatgtggacacgacaataactccgttcttggatgttaaaactattttgacaatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG

Basic information

species Zea mays
transcript GRMZM2G011078_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011078_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 10
gtgagtgagtgagtctaccgctattattcagtctgaatccagtaaatcagaattccacaggataatagtacctatatttcctgcaaagacaaattgtacatacatcaaaagcatctcgcatggcatgttttatgtggacacgacaataactccgttcttggatgttaaaactattttgacaatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG
                                                                         ||   || | |     |||||  ||||       || ||| |         ||  |   | ||        ||| | |  | ||||  ||  | |   | |          |  ||||||||||||||||||| |||| |||||||||| | ||  ||||| | ||| | ||||| ||||||
-------------------------------------------------------------------------atgcctcatccttttgcaaatactaca------gaatgcaacctaagcaatattctgcttctg--------aatgatt--gatcttttattatgattttctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG

upper sequence: GRMZM2G011078_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT1G61250.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgagtgagtgagtctaccgctattattcagtctgaatccagtaaatcagaattccacaggataatagtacctatatttcctgcaaagacaaattgtacatacatcaaaagcatctcgcatggcatgttttatgtggacacgacaa-taactccgttcttggatgttaaaactattttgacaatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG
                                                                                          ||  | | |  ||      |  ||||   |   ||  | | |  |  |  |   |  | | |   |   |  ||| |   | ||| |   |  | |  |||| |||||||||||||| |||||||| |||||||| ||  |  || | ||| | ||||| ||||||
----------------------------------------------------------------------------------------gtaagctct-ctcaccctttgatgatctta-aaaacaactctaagataaaagcctgatctgattatatgtatcaatgatctga-tatctgttctgtttatagATATTCTACTTCATTGGGTTTGCATTTTTCTGCCTCGAATCAGTGGTTAGCATCTGGGTTATTCAG

upper sequence: GRMZM2G011078_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT1G61250.2 (Arabidopsis thaliana), 3'ss of exon 10
gtgagtgagtgagtctaccgctattattcagtctgaatccagtaaatcagaattccacaggataatagtacctatatttcctgcaaagacaaattgtacatacatcaaaagcatctcgcatggcatgttttatgtggacacgacaa-taactccgttcttggatgttaaaactattttgacaatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG----------------------------------
                                                                                          ||  | | |  ||      |  ||||   |   ||  | | |  |  |  |   |  | | |   |   |  ||| |   | ||| |   |  | |  |||| |||||||||||||| |||||||| |||||||| ||  |  || | ||| | ||||| ||||||                                  
----------------------------------------------------------------------------------------gtaagctct-ctcaccctttgatgatctta-aaaacaactctaagataaaagcctgatctgattatatgtatcaatgatctga-tatctgttctgtttatagATATTCTACTTCATTGGGTTTGCATTTTTCTGCCTCGAATCAGTGGTTAGCATCTGGGTTATTCAGGTCTGTCTCTTCAACTCCCATCACTATATTATCA

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|31362151|gb|CD446508.1|CD446508
EST:     CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGG                         ATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC
genomic: CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGGgtgagtgagt ... caatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC
EST: gi|71440938|gb|DR821988.1|DR821988
EST:     CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGG                         ATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC
genomic: CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGGgtgagtgagt ... caatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC
EST: gi|24763111|gb|CA398294.1|CA398294
EST:     CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGG                         ATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC
genomic: CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGGgtgagtgagt ... caatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC
EST: gi|76280657|gb|DV020225.1|DV020225
EST:     CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGG                         ATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC
genomic: CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGGgtgagtgagt ... caatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC
EST: gi|89760515|gb|DY688892.1|DY688892
EST:     CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGG                         ATCTTTTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC
genomic: CGGGATTTTGCCAGCAATCAGCTTGATAGGCGACAGCGTCATTGTTGGGgtgagtgagt ... caatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggacacgacaataactccgttcttggatgttaaaactattttgacaatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG
                                                tctcc  CT-rich tract
                           atgttaaaactatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgagtgagtctaccgctattattcagtctgaatccagtaaatcagaattccacaggataatagtacctatatttcctgcaaagacaaattgtacatacatcaaaagcatctcgcatggcatgttttatgtggacacgacaataactccgttcttggatgttaaaactattttgacaatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG