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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgcttcttccttatgccaaggcctgtgttttcttcttgtactgctgacatcgtttgatatttttgtattgccctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT

Basic information

species Zea mays
transcript GRMZM2G061620_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061620_T05 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g24200.1 (Oryza sativa), 3'ss of exon 9
gtatgcgcttcttccttatgccaaggcctgtgttttcttcttgtactgctgacatcgtttgatatttttgtattgccctgaaccagGA---TGCTGGATCAGATGGCAGATGCAA---CTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT
|||||   |  |   |  |   |       | |||||||||  | |   ||   |  ||    || |||   ||   |||||||||||   |||| || ||| |  |||| ||||   |  ||||||| ||||| |||||||||||||||||||| |||||||||
gtatgtcttaatctttgcttttatcataactcttttcttctgatgcgtttgctgt-attaacaatctttccctt--tctgaaccagGAATTTGCTAGACCAGTTTCCAGAGGCAATGCCACAGACCATAGCAGTTACTCCAGAGGAGAATGAAGCCATACTTCGT
















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|4804466|gb|AI665336.2|AI665336
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|33103619|gb|CF063579.1|CF063579
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGAT
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGAT
EST: gi|33092724|gb|CF052718.1|CF052718
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|32944591|gb|CF049410.1|CF049410
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|88748485|gb|DY532626.1|DY532626
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|211179390|gb|FL472344.1|FL472344
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|33103634|gb|CF063594.1|CF063594
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|60396214|gb|DN229083.1|DN229083
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|16922733|gb|BM075725.1|BM075725
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACAAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|211167569|gb|FL481155.1|FL481155
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|6431881|gb|AW172085.1|AW172085
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|101401580|gb|EB822466.1|EB822466
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|211510600|gb|FL470556.1|FL470556
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|16927288|gb|BM080357.1|BM080357
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|32850730|gb|CD990411.1|CD990411
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|211460054|gb|FL445989.1|FL445989
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|211460055|gb|FL445990.1|FL445990
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|33104092|gb|CF064052.1|CF064052
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|16926213|gb|BM079281.1|BM079281
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|78073733|gb|DV502167.1|DV502167
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|211501745|gb|FL041143.1|FL041143
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|78078954|gb|DV507366.1|DV507366
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|60355834|gb|DN222807.1|DN222807
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|60339280|gb|DN206253.1|DN206253
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|18173700|gb|BM349088.1|BM349088
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|76280697|gb|DV020265.1|DV020265
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|76288771|gb|DV028339.1|DV028339
EST:     TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
EST: gi|4966941|gb|AI691754.1|AI691754
EST:     TTTATGCGGTTGATTAGTGAGCCCCTAGAGGGAGACGAAGAGAATGAAAT                         GATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA
genomic: TTTATGCGGTTGATTAGTGAGCCACTAGAGGGAGACGAAGAGAATGAAATgtatgcgctt ... cctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttcttcttgtactgctgacatcgtttgatatttttgtattgccctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT
                                         ttgccct  CT-rich tract
                          tttgatatttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcgcttcttccttatgccaaggcctgtgttttcttcttgtactgctgacatcgtttgatatttttgtattgccctgaaccagGATGCTGGATCAGATGGCAGATGCAACTGAGACCATTGCAGTCACTCCAGAGGAGAATGAAGCTATACTTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC