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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgcaagcatcctcttcatgatgctatgttagcatagtgtactattagctcgtgcccactctatgtcaaaatatgtacactgttccaaatttaa...

Basic information

species Zea mays
transcript GRMZM2G063851_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 6
GTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgcaagcatcctcttcatgatgctatgttagcatagtgtactattagctcgtgcccactctatgtcaaaatatgtacactgttccaaatttaa-
||||||||||| |||||||||||||||||||||||||||||||||||  | ||||| || || ||||||  |||| || |         | ||| | ||  | ||||| | ||  |  |  |  ||   | | | | |    |||| |  |   |   |  |  || 
GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgtaaactataatgctacgataccataatggcataatatagaagcaaatt-tggatattttgtctatgtatatcttgaaattggaatgtgcaaa

upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 5
GTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgcaagcatcctcttcatgatgctatgttagcatagtgtactattagctcgtgcccactctatgtcaaaatatgt-acactgttccaaatttaa-----
|||||||| || |||||||| |||| |||||||||||||||||||||  | ||||| || |||||||||  |||| ||     || |  ||| | ||||| || |||| | ||  |  ||   ||||  | | | | |  | |||| |   | ||| | | |  | |     
GTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAGgtatacttgtaa-----ctatgtatggttctatgataccataatataaaagcagaa-gtgcttattttgtctatatatatcttgtaatgtgcaatagatgaaaaat

upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 6
GTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgcaagcatcctcttcatgatgctatgttagcatagtgtactattagctcgtgcccactctatgtcaaaatatgtacactgttccaaatttaa----------------------------
||  |||||||||||||||||||||||||| ||||||||||||| ||  | ||||| || || |||||| | |    |  |  ||||  ||   | ||   |||| | ||    |  ||| |   |   |    |  |       |     |||||| ||   |                              
GTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAGgtactgt----ataactctctgtatatagttacaatagcttggttagatcctagatatagaatatatcaaat--gctcctccttcctgttctaaggctgttgatgcaattatcttatcattatttcag

upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 5
GTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgcaagcatcctcttcatgatgctatgttagcatagtgtactattagctcgtgcccactctatgtcaaaatatgtacactgttccaaatttaa
|| ||||||||||||||||||||||||||| | || |||||||| ||  | |||||| |||| ||||||   ||  ||   |  ||     |||  | |    |     | |   |||||    |    |   ||||  |  || | |    |||  ||       
GTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAGgtatggttataattttgatcacatagataattttcaggtcagatcttgaattagaat-tatataacatatgatattatcttt----tgtatcag------

upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 6
lower sequence: EFJ29959 (Selaginella moellendorffii), 5'ss of exon 5
GTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgcaagcatcctcttcatgatgctatgttagcatagtgtactattagctcgtgcccactctatgtcaaaatatgtacactgttccaaatttaa
| | ||||||||||| ||||||| |  || |||||||||||||| ||||| || ||||| || |||||| ||  | |   ||  | ||| |  |||| | | ||| |  |   | |  ||                                              
GCCATTGGTGGAATGCGAGGGATTAAAGGCATGCTTTGGGAAACGTCCCTGCTCGATCCTGAAGAGgtagtcaaggatttatt-tgttctt--tgctgtttcagcgtccttggcaaacag----------------------------------------------

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|211507876|gb|FL228171.1|FL228171
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTG
EST: gi|211059244|gb|FL131321.1|FL131321
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|93284646|gb|EB676910.1|EB676910
EST:     AGGGATGACTGGAATGCTTTTGGAAACATCCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTC
genomic: AGGGATGACTGGAATGCTTTGGGAAACATCCC-TACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTC
EST: gi|211510249|gb|FL228196.1|FL228196
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAAT
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAAT
EST: gi|148974563|gb|EE025351.2|EE025351
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|211510246|gb|FL228193.1|FL228193
EST:     AGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCCAGAGGAG                         GGTATTCGTTTTAGGGG
genomic: AGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCC-AGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGG
EST: gi|211507880|gb|FL228175.1|FL228175
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCC
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCC
EST: gi|211507878|gb|FL228173.1|FL228173
EST:     GGGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAA
EST: gi|211510237|gb|FL228184.1|FL228184
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGC-AAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|211507873|gb|FL228168.1|FL228168
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTTCA-TTCCAGAATGCCAAAAAGTGCTGCC
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCT-CAATTCCAGAATGCCAAAAAGTGCTGCC
EST: gi|211507875|gb|FL228170.1|FL228170
EST:     GAGGGATGACTGGAATGCTTTNGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGC-TCTCAATTCCAGAAT
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAAT
EST: gi|211505527|gb|FL228166.1|FL228166
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGC
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgcaagcatcctcttcatgatgctatgttagcatagtgtactattagctcgtgcccactctatgtcaaaatatgtacactgttccaaatttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG