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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacgcaaatattcagagaggtgttcttttaagaatatatgctttcctccttaatcatcgatcatcctgtaataacttggttctctgttattttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGAAGCTAATGGTGATATTCTTGTTTTCATCTCATCATTCAACCCAATGAAG

Basic information

species Zea mays
transcript GRMZM5G806449_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g56850.1 (Oryza sativa), 3'ss of exon 13
----tgacgcaaatattcagagaggtgttcttttaagaatatatgctttcctccttaatcatcg-atcatcctgtaataacttggttctctgttattttcaat-agCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGAAGCTAATGGTGATATTCTTGTTTTCATCTCATCATTCAACCCAATGAAG
        |||  |||       | || | | || ||| ||| ||||||  |||  ||||||||  |||  |    ||||| |||||   | || | || ||| ||||| ||||||||||| ||||||||| | || ||| | ||||| ||||||||||| ||  | ||| ||||||||| ||  ||    |||||||||||||||
tattcagtgcatttatggctgctgctgctttctttagattatctgcttt--tccacaatcatcgtgtcactc----ataacatggtttctttttttgttgaattagCATCCCACCACTATCAGTAGTGGGCTTGAGTGAACAGCAGGCTTTGGAGGAAGCCAAGAGCGATGTTCTTGTTTACACTTCCAGCTTCAACCCAATGAAG

upper sequence: GRMZM5G806449_T03 (Zea mays), 3'ss of exon 13
lower sequence: AT3G24170.2 (Arabidopsis thaliana), 3'ss of exon 13
-tgac-gcaaatattcagagaggtgttcttttaagaatatatgctttcctccttaatcatcgatcatcctgtaataacttggttctctgttattttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGAAGCTAATGGTGATATTCTTGTTTTCATCTCATCATTCAACCCAATGAAG
 |  | || | | |  | | |   ||  | | |    |||||   |    | ||    |   ||  |    |  ||  || |||  ||  | | |||   ||||| ||||||||| |||||||||| |||||||||||| | ||  | ||  |||| |  ||||||||||| || |||| ||||   || || |||||||||
atatctgctactctggaaatatcagtattctcatagttatatagatattacattttctaaatattttttatttttatttttgtttccttatgtcttc--cagCATACCACCACTAGCTGTAGTGGGTCTCAGCGAAGAAGAAGCAGTAGAACAAGCAACCGGTGATATTCTGGTCTTCACCTCAGGCTTTAATCCAATGAAG
















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|19350945|gb|BM895477.1|BM895477
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|76293304|gb|DV032872.1|DV032872
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|19350946|gb|BM895478.1|BM895478
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|32845839|gb|CD985520.1|CD985520
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTCTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|211368053|gb|FL471715.1|FL471715
EST:     GGCCAGCAAGTTAAGCTTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|47961792|gb|CN844501.1|CN844501
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTGGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|58030045|gb|CX725472.1|CX725472
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|37380707|gb|CF627182.1|CF627182
EST:     GGCCAGCAAGTAAAGCCTGATCACAGAGATGTTCTTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|71757895|gb|DR955832.1|DR955832
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|76012766|gb|DT939936.1|DT939936
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|16916633|gb|BM072928.1|BM072928
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|110942635|gb|EE162792.1|EE162792
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|31405874|gb|CD484606.1|CD484606
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|91056621|gb|EB167039.1|EB167039
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTTTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|56382549|gb|CV985218.1|CV985218
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|37381448|gb|CF627611.1|CF627611
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|6095693|gb|AW120360.1|AW120360
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|31664369|gb|CD573094.1|CD573094
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|37377035|gb|CF625088.1|CF625088
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|14243079|gb|BG840745.2|BG840745
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|16927664|gb|BM080733.1|BM080733
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|31664100|gb|CD573280.1|CD573280
EST:     GCCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGCCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|32939543|gb|CF044362.1|CF044362
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGGCCTCAGCGAAGAACAGGCCTTGGAGG
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGG-CCTCAGCGAAGAACAGGCCTTGGAGG
EST: gi|30088227|gb|CB886432.1|CB886432
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|31611972|gb|CD568594.1|CD568594
EST:     CCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: CCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|148937230|gb|EC881412.2|EC881412
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|71311903|gb|DR792430.1|DR792430
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|149077607|gb|EE166307.2|EE166307
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCTTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
EST: gi|6031612|gb|AI668515.2|AI668515
EST:     GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC                         CATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA
genomic: GGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTCgttagtcaca ... ttttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctccttaatcatcgatcatcctgtaataacttggttctctgttattttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGAAGCTAATGGTGATATTCTTGTTTTCATCTCATCATTCAACCCAATGAAG
                        taataac  putative branch site (score: 1)
                                   ttctctgttattttc  putative PPT
                                        tgttattttcaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacgcaaatattcagagaggtgttcttttaagaatatatgctttcctccttaatcatcgatcatcctgtaataacttggttctctgttattttcaatagCATTCCACCACTATCTGTAGTGGGCCTCAGCGAAGAACAGGCCTTGGAGGAAGCTAATGGTGATATTCTTGTTTTCATCTCATCATTCAACCCAATGAAG

- acgcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttct