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

gtttgcaaataggcaaatgagcaatattgttcctctacttattaattacgattgatgatcaatgtggcctgaaggcaaaaaaatgtttcaaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGAGTACCACTTGGAATAATGACGATGAAG

Basic information

species Zea mays
transcript GRMZM2G155962_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155962_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g32150.1 (Oryza sativa), 3'ss of exon 5
gtttgcaaataggcaaatgagcaatat---------tgttcctctacttattaattacgattgatgatcaatgtggcctga---aggcaaaaaaatgtttcaaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGAGTACCACTTGGAATAATGACGATGAAG
||||| |    ||||| || ||  |||         |||||   |   | || ||||   |  |||||        |   |   ||   | ||||||  | |||   | ||||||| ||||||||||| |||||||||||  | ||||| ||||||||||||| |||| ||||||| |||  |||||||
gtttgtagg--ggcaactgtgctgtataaattttcatgttctcttgaatgttgattatcgtaaatgatttggacttcacaagtcagaacacaaaatgccttaaaattatagATGACAAATGAGGTTGGGAGGTCATTATTCGCTAAGGCTGGAGAACTTGGAGCACCAGTTGGAATCATGGTGATGAAG
















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|93284051|gb|EB676315.1|EB676315
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|60397566|gb|DN230382.1|DN230382
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|20507977|gb|BQ279847.1|BQ279847
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGGGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|21987683|gb|BQ779211.1|BQ779211
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGGGAACTTGGA
genomic: A-TACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|76909087|gb|DV163216.1|DV163216
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|101390398|gb|EB817133.1|EB817133
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|88748896|gb|DY533037.1|DY533037
EST:     ACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
genomic: ACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|26456812|gb|CA828395.1|CA828395
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGGGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|211322964|gb|FL249422.1|FL249422
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGGGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|78090807|gb|DV519181.1|DV519181
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|26558292|gb|CA830527.1|CA830527
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGGGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|76909089|gb|DV163217.1|DV163217
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|60357568|gb|DN224541.1|DN224541
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGA
EST: gi|211320798|gb|FL249415.1|FL249415
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGC
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGC
EST: gi|211320801|gb|FL249418.1|FL249418
EST:     AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGSCATCTGGTCAAAAG                         ATGACCAATGAGGTTGGAAGG
genomic: AATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAAAAGgtttgcaaat ... aaataaacagATGACCAATGAGGTTGGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacgattgatgatcaatgtggcctgaaggcaaaaaaatgtttcaaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGAGTACCACTTGGAATAATGACGATGAAG
                                aaaaaaatgtttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcaaataggcaaatgagcaatattgttcctctacttattaattacgattgatgatcaatgtggcctgaaggcaaaaaaatgtttcaaataaacagATGACCAATGAGGTTGGAAGGTCATTATTTTCGAAGGCAGGAGAACTTGGAGTACCACTTGGAATAATGACGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG