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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_T04
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|51592469|gb|CV071615.1|CV071615
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|21480820|gb|BQ577503.1|BQ577503
EST:     TGATCCAGAGGAG                         GGTATTCGTGTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGGC
genomic: TGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGT-TTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCC
EST: gi|32868179|gb|CF007861.1|CF007861
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|78109451|gb|DV527867.1|DV527867
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|67040702|gb|CO466957.1|CO466957
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|74035022|gb|DT535512.1|DT535512
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA

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