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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttccatttgcttgttcatttgttttcccgcttcattttaccttttgattaatggaagcaatatttggattttgacagtggaagaactacacat...

Basic information

species Zea mays
transcript GRMZM2G153704_T07
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153704_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g04190.2 (Oryza sativa), 5'ss of exon 7
AAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttccatttgcttgttcatttgttttcccgcttcattt--taccttttgattaatggaagcaatatttggattttgacagtggaagaactacacat
|||| |||||| |||||||| | |||||||| |||||||| ||||||||||||||||| ||| || |||||||||| |||||||||||||| ||||| |||| ||||||     |  || ||   |  |  | | |||||||||  | ||||||   |  |        |      |   | |   |||   | |  |    
AAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAGGAAACCCTGCTTGgtgagtttttgtcctagttcttttctcctgcttctgcttcatttagtgccttttacattcttatctggttgcacaaacaatcattttggtttatcgtctt--

upper sequence: GRMZM2G153704_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA13G07780.1 (Glycine max), 5'ss of exon 7
AAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttccatttgcttgttcatttgttttcccgcttcattttaccttttgattaatggaagcaatatttggattttgacagtggaagaactacacat--
||||||||||  | || ||  | ||||||||||||||||| |||||||| ||||||   ||  || | |||||  |||||||||||||||| |||   |||||     |   ||  | |   || |   |||     | ||        |  |  ||  ||    |||||||  |  |   |  |    || ||        
AAATTCGTGGTGCGCTAGGATCTGTTAATCAACTTTTTATATGCATTGGGATTCTTCTGGCACTGGTGGCTGGGCTGCCTCTGGCAGGAAACCCTATATGgtattgagttgtttcaccttaccact--atttgtttttgcagggaggggtgagcataggggtgtgaatattttaacctaacctctttttgagctgttttctt

upper sequence: GRMZM2G153704_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 5'ss of exon 7
AAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttccatttgcttgttcatttgttttcccgcttcattttaccttttgattaatggaagcaatatttggattttgacagtggaagaactacacat----
||||||||||  | |||||  | || ||||||||||||||||| ||||| ||||||||||| ||| | |||||||| ||||| ||  |||| |||   |||||  || | | | |  |  |||||||| | |  |  |  ||             |  ||| |||       |   |  | ||    || ||   || |     
AAATTCGTGGTGCGCTTGGGTCTGTCAATCAACTTTTTATTTGTATTGGGATTCTTGCAGCATTGGTGGCTGGATTACCTCTAGCCAGAAACCCTCTATGgta--ttcttcttgtcatatttcatttgctatatc--tatatgcaggaagaaagcttttggtagcttagcgagagataagtcaactaaataaactcaaaagcac

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|60400456|gb|DN233263.1|DN233263
EST:     ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTG                         GTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
genomic: ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttc ... atttaatcagGTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
EST: gi|32832104|gb|CD971782.1|CD971782
EST:     ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTG                         GTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
genomic: ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttc ... atttaatcagGTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
EST: gi|61119088|gb|DN560049.1|DN560049
EST:     CTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTG                         GTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
genomic: CTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttc ... atttaatcagGTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
EST: gi|67035008|gb|CO463541.1|CO463541
EST:     ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTG                         GTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
genomic: ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttc ... atttaatcagGTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
EST: gi|67037358|gb|CO464198.1|CO464198
EST:     ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTG                         GTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
genomic: ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttc ... atttaatcagGTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
EST: gi|211050167|gb|FL124868.1|FL124868
EST:     ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTG                         GTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
genomic: ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttc ... atttaatcagGTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
EST: gi|32847646|gb|CD987327.1|CD987327
EST:     ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTG                         GTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
genomic: ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttc ... atttaatcagGTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
EST: gi|32835079|gb|CD974757.1|CD974757
EST:     ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTG                         GTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
genomic: ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttc ... atttaatcagGTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
EST: gi|22545719|gb|BU098078.1|BU098078
EST:     ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTG                         GTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT
genomic: ATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttc ... atttaatcagGTGGAGGACAATGTTTGGAATTGCTGTAGTTCCATCCATTCTGCTGGCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAGGAAATCCTGCCTGgtaagttttccatttgcttgttcatttgttttcccgcttcattttaccttttgattaatggaagcaatatttggattttgacagtggaagaactacacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA