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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGGCATTGGTGCCGACGGCGTCATCTTCGTCATGCCAGGGGTCAATGATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgtctccaccatttcatcacaatactgaattctattgcacggtcgtggatgtaatgttctcgcaattcttattggtagccattcttctcagcc...

Basic information

species Zea mays
transcript GRMZM2G130332_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130332_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g37960.1 (Oryza sativa), 5'ss of exon 2
CTTCGGCATTGGTGCCGACGGCGTCATCTTCGTCATGCCAGGGGTCAATGATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgtctccaccatttcatcacaatactgaattctattgcacggtcgtggatgtaatgttctcgcaattcttattggtagccattcttctcagcc------
||||||| | || |||||||| || |||||||||||||| ||||||||||  || |||||||||||||||||||||||||| |||||||| ||||| |||||| ||         ||||| |||  |   | ||  |  ||    | |     || |||     | | |  ||     | |  |  | |   ||  |         
CTTCGGCGTCGGCGCCGACGGTGTGATCTTCGTCATGCCGGGGGTCAATGGCGCGGACTACACCATGAGGATCTTCAACTCGGACGGCAGTGAGCCGGAGgtgagcaat------ccattgcatttctgcagtgcgtgataggaaatgtattcgggtgttggtgttttgtgatatccgtagtgattcgtcaatcataaatgcaatg

upper sequence: GRMZM2G130332_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ30110 (Selaginella moellendorffii), 5'ss of exon 2
CTTCGGCATTGGTGCCGACGGCGTCATCTTCGTCATGCCAGGGGTCAATGATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgtctccaccatttcatcacaatactgaattctattgcacggtcgtggatgtaatgttctcgcaattcttattggtagccattcttctcagcc
||| ||| | || | ||| || |||||||| |  ||||| ||   | | |    ||||||| ||||| |||||| |||||| |||||||| ||||||||||||   | |  |  ||  |||  |  | ||  ||  || | || |  |||  |   |                                           
CTTTGGCGTGGGAGGCGATGGTGTCATCTTTGCTATGCCGGGAACCCAAGGCTGCGACTACTCCATGCGGATCTACAACTCCGACGGCAGTGAGCCAGAGgtgaatgagagttgactctttt-tagcgat--tgtcttgtgtt-cttggttctctctag-----------------------------------------

upper sequence: GRMZM2G130332_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ08289 (Selaginella moellendorffii), 5'ss of exon 1
CTTCGGCATTGGTGCCGACGGCGTCATCTTCGTCATGCCAGGGGTCAATGATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgtctccaccatttcatcacaatactgaattctattgcacggtcgtggatgtaatgttctcgcaattcttattggtagccattcttctcagcc
||| ||  | || | ||| || |||||||| |  ||||| ||   | | |    ||||||| ||||| | |||| |||||| |||||||| ||||||||||||   | |  |  ||  |||  |  | ||  ||  || | || |  |||  |   |                                           
CTTTGGTGTGGGAGGCGATGGTGTCATCTTTGCTATGCCGGGAACCCAAGGCTGCGACTACTCCATGCGAATCTACAACTCCGACGGCAGTGAGCCAGAGgtgaatgagagttgactctttt-tagcgat--tgtcttgtgtt-cttggttctctctag-----------------------------------------

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|148986800|gb|EE030596.2|EE030596
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|87155814|gb|DY400603.1|DY400603
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|91052902|gb|EB163320.1|EB163320
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|93014173|gb|EB639693.1|EB639693
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|91878422|gb|EB408379.1|EB408379
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|148961368|gb|EE012101.2|EE012101
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|71324621|gb|DR799009.1|DR799009
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|211442708|gb|FL002350.1|FL002350
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|71769300|gb|DR967237.1|DR967237
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|78088914|gb|DV517307.1|DV517307
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|76286735|gb|DV026303.1|DV026303
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|78088792|gb|DV517185.1|DV517185
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|50337846|gb|CO532972.1|CO532972
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|22133843|gb|BQ833933.1|BQ833933
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|71329026|gb|DR801212.1|DR801212
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|26558147|gb|CA830382.1|CA830382
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|22715577|gb|BU197842.1|BU197842
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|211442703|gb|FL002345.1|FL002345
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCCGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|76014966|gb|DT942136.1|DT942136
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|101395236|gb|EB819548.1|EB819548
EST:     TGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGA
genomic: TGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCC-AGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGA
EST: gi|148961806|gb|EE012586.2|EE012586
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|71443835|gb|DR824885.1|DR824885
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|211442709|gb|FL002351.1|FL002351
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|26559567|gb|CA831802.1|CA831802
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|101383177|gb|EB813643.1|EB813643
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|148970899|gb|EE021693.2|EE021693
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|74233526|gb|DT641440.1|DT641440
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
EST: gi|211442702|gb|FL002344.1|FL002344
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGC
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGC
EST: gi|76017579|gb|DT944749.1|DT944749
EST:     ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAG                         ATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA
genomic: ATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgt ... ttttcatcagATGTGTGGTAATGGAGTCCGTTGCTTTGCTCGGTTTATAGGCGAACTTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGGCATTGGTGCCGACGGCGTCATCTTCGTCATGCCAGGGGTCAATGATGCCGACTACACCATGAGGATCTTCAACTCTGACGGCAGCGAGCCAGAGgtgcgcgtgtctccaccatttcatcacaatactgaattctattgcacggtcgtggatgtaatgttctcgcaattcttattggtagccattcttctcagcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT