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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATACGACCAGCTTAGGGCACCGGTTGGGAGGGTATACTTCACCGGCGAGCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagtacacttgaccttcccaacaagattactagtgtagtgacataggcttgcacttacggcgtgaaatttcttccattcttgtgtctctgttgatggcag

Basic information

species Zea mays
transcript GRMZM2G034152_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034152_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g09810.1 (Oryza sativa), 5'ss of exon 6
GAATACGACCAGCTTAGGGCACCGGTTGGGAGGGTATACTTCACCGGCGAGCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagtacacttgaccttcccaacaagattactag---tgtagtgacataggcttgcacttacggcgtgaaatttcttccattcttgtgtctctgttgatggcag
                  || ||| ||| |||||| ||||||||||| |||||||| |||||| ||||||||||||||||||||||||  |||||| ||||| | ||  |  |     ||| | ||| |   | || ||   | || ||  | ||  |||  ||||         |||  |  | ||  || |||              
------------------GCCCCGATTGAGAGGGTTTACTTCACCGGTGAGCACACAAGCGAGTACTACAATGGCTATGTCCATGGAGGTTATCTTGCAGgtatacatatctat---gcctactcaagagcctgacaagatttctaatgctaaagttttgtgctta---------attattcgcttttctgcgtcag------------

upper sequence: GRMZM2G034152_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv01s0127g00780.t01 (Vitis vinifera), 5'ss of exon 8
GAATACGACCAGCTTAGGGCACCGGTTGGGAGGGTATACTTCACCGGCGAGCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagtacacttgaccttcccaacaagattactagtgtagtgacataggcttgcacttacggcgtgaaatttcttccattcttgtgtctctgttgatggcag
                  ||||| ||||||||||| |||||||| |||||||| ||||||||| ||| ||| || ||||| ||||| || |||||| ||||| ||      || ||  | |    |||    || | |  | ||   |      |   || | | |   |||||| |           |   |  |  |       
------------------GCACCTGTTGGGAGGGTCTACTTCACAGGCGAGCATACCAGCGAGTACTTCAACGGTTATGTTCATGGCGCATATCTTGCAGgtttgtcttatcatttatcatattaaactgcctt-ccacagcagaagccagcagtcatacgtgctg---gaaattacaatagaaaaaattctttcgcag-------

upper sequence: GRMZM2G034152_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv01s0127g00800.t01 (Vitis vinifera), 5'ss of exon 8
GAATACGACCAGCTTAGGGCACCGGTTGGGAGGGTATACTTCACCGGCGAGCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagtacacttgaccttcccaacaagattactagtgtagtgacataggcttgcacttacggcgtgaaatttcttccattcttgtgtctctgttgatggcag
                  ||||| ||||| ||||| |||||||| ||||| ||||||||| | ||||||||||| || || || || ||||| ||| ||||| ||    | |   | || |  | || |   |  | |    | |   || |   | |  | |   |  |||| |  |  ||                        
------------------GCACCTGTTGGAAGGGTTTACTTCACAGGCGAACACACCAGCCAACACTACAATGGTTACGTTCACGGTGCCTACCTTGCAGgtttgtt--ttcttgttacataactaatagcctctcaaacaca-tacaatggaaattc--taagacccggaaaatattcacag-----------------------

upper sequence: GRMZM2G034152_T02 (Zea mays), 5'ss of exon 6
lower sequence: PP1S20_19V6.1 (Physcomitrella patens), 5'ss of exon 7
GAATACGACCAGCTTAGGGCACCGGTTGGGAGGGTATACTTCACCGGCGAGCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagtacacttgaccttcccaacaagattactagtgtagtgacataggc-ttgcacttacggcgtgaaatttcttccattcttgtgtctctgttga-tggcag
                  || |||||    |   | |||||||||||||||||||| |||||| | |||||||||||||| |||||  | ||  |   ||||       ||  ||| |    |  | || |  || |  |   | | | |  || || |   |     |  | | ||   |     |||   |    | || | ||  
------------------GCGCCGGTCCAAACTATCTACTTCACCGGCGAGCACACAAGCGAGGAGTACAATGGCTATGTTCATGGCCCTTACTTGCAAGgtactt---tattctttaatgactaagcacg--tattgata-ggcgtcttgagcatttcgactgtccagcaacagttgagcgtggtttgaaacgagttagaattgc--

upper sequence: GRMZM2G034152_T02 (Zea mays), 5'ss of exon 6
lower sequence: EFJ34103 (Selaginella moellendorffii), 5'ss of exon 8
GAATACGACCAGCTTAGGGCACCGGTTGGGAGGGTA---TACTTCACCGGCGAGCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctg-caagtacacttgaccttcccaacaagattactagtgtagtgacataggcttgcacttacggcgtgaaatttcttccattcttgtgtctctgttgatggcag
   |  || |   |    || ||| |   | | |     ||||||| ||| |||||||||  |||||||||||||||||| ||||| ||||| ||       |||  | |  |   |    | ||      ||  |     | | | |    ||  ||| |||                                               
---TTTGAGCGAATCCAAGCGCCGCTCAAGGGAGCGCTCTACTTCAGCGGAGAGCACACCCACGAGCACTACAATGGCTACGTCCACGGAGCTTACTACAGTGgtgagtcttgcggaagaaagctcgttttcagtacc-tgactctcggaggatttgctcgcaag---------------------------------------------

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|78074436|gb|DV502870.1|DV502870
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|76909565|gb|DV163430.1|DV163430
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|71430611|gb|DR811661.1|DR811661
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|71321689|gb|DR797534.1|DR797534
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|37390923|gb|CF632699.1|CF632699
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|28985050|gb|BQ539313.2|BQ539313
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|15499389|gb|BI595902.1|BI595902
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|13558946|gb|BG550301.1|BG550301
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAGCTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|71320815|gb|DR797125.1|DR797125
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|18178524|gb|BM379734.1|BM379734
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|71759319|gb|DR957256.1|DR957256
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|78082935|gb|DV511328.1|DV511328
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|18181175|gb|BM382385.1|BM382385
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTTTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|31998417|gb|CD662068.1|CD662068
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAGCTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|86471094|gb|DY237464.1|DY237464
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|15427007|gb|BI542829.1|BI542829
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|71417002|gb|DR803884.1|DR803884
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTTTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|86470055|gb|DY236425.1|DY236425
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTTTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|149085906|gb|EE175434.2|EE175434
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|4609833|gb|AI600672.1|AI600672
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|148947285|gb|EC892659.2|EC892659
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|14244049|gb|BG841780.2|BG841780
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|78092544|gb|DV520918.1|DV520918
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|15353025|gb|BI502636.1|BI502636
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|148955995|gb|EC901723.2|EC901723
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTTTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|148934894|gb|EC878941.2|EC878941
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTTTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|83278631|gb|DV942639.1|DV942639
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|110524569|gb|EE028753.1|EE028753
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA
EST: gi|71758095|gb|DR956032.1|DR956032
EST:     GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAG                         GTATCGACTCCGCTGAAATTTTCATCAACTGCGCCCAGAAAAAGATGTGCA
genomic: GCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagt ... ttgatggcagGTATCGACTCCGCTGAAATTCTCATCAACTGCGCCCAGAAAAAGATGTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATACGACCAGCTTAGGGCACCGGTTGGGAGGGTATACTTCACCGGCGAGCACACCAGCGAGCACTACAATGGCTATGTCCATGGAGCCTATCTTTCAGgtctgcaagtacacttgaccttcccaacaagattactagtgtagtgacataggcttgcacttacggcgtgaaatttcttccattcttgtgtctctgttgatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA