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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accacagcatgccactgtttcctttcttttgtcagtttttatttccccgctgggtcctgtacctccatgtttcctcactggggttaccattttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCTGCGATGGAGGAGAAGGCTATGGCAAATGGAGCAGCGACTGCTGATGTTG

Basic information

species Zea mays
transcript GRMZM5G830403_T02
intron # 1
splice site 3'
intron type U2

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|211534597|gb|FL330659.1|FL330659
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211522483|gb|FL328363.1|FL328363
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCAGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211409154|gb|FL322201.1|FL322201
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|21088797|gb|BQ401110.1|BQ401110
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCGCCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211055289|gb|FL324094.1|FL324094
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211179126|gb|FL348509.1|FL348509
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211109456|gb|FL307940.1|FL307940
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211132698|gb|FL358675.1|FL358675
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211133470|gb|FL349785.1|FL349785
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|20811073|gb|BQ295551.1|BQ295551
EST:     CCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: CCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211409514|gb|FL337219.1|FL337219
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211340350|gb|FL350499.1|FL350499
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211007802|gb|FL355793.1|FL355793
EST:     NCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|29946030|gb|CB815943.1|CB815943
EST:     CCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: CCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211250639|gb|FL329634.1|FL329634
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|22819871|gb|BU499961.1|BU499961
EST:     CCTTCTCAGGCGG-CCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAG-AATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: CCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|20513075|gb|BQ280261.1|BQ280261
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211463259|gb|FL358478.1|FL358478
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211195334|gb|FL321654.1|FL321654
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211320079|gb|FL327300.1|FL327300
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|5058601|gb|AI737077.1|AI737077
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|29946028|gb|CB815942.1|CB815942
EST:     CGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: CGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211406448|gb|FL317383.1|FL317383
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|20507251|gb|BQ279549.1|BQ279549
EST:     ACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: ACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211149766|gb|FL359578.1|FL359578
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211174278|gb|FL481203.1|FL481203
EST:     CGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: CGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211333743|gb|FL358886.1|FL358886
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211495656|gb|FL364221.1|FL364221
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211275700|gb|FL312170.1|FL312170
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211393423|gb|FL311882.1|FL311882
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
EST: gi|211192602|gb|FL309861.1|FL309861
EST:     GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAG                         TTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT
genomic: GCTCCACTCCCTTCTCAGGCGGCCCCCTGCTGCTCACCGCCCAGCTCCAGgtacgcgcga ... tttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgctgggtcctgtacctccatgtttcctcactggggttaccattttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCTGCGATGGAGGAGAAGGCTATGGCAAATGGAGCAGCGACTGCTGATGTTG
                                            ttttaac  putative branch site (score: 2)
                                         ccatttt  CT-rich tract
                                           attttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accacagcatgccactgtttcctttcttttgtcagtttttatttccccgctgggtcctgtacctccatgtttcctcactggggttaccattttaacacagTTATTAGAGAAATAAGGGTCGGCTTGGTTGCCCGAGGCCTACCCAGCGCCTGCGATGGAGGAGAAGGCTATGGCAAATGGAGCAGCGACTGCTGATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT