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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAACAAGAGCAGCCTCATGATGGTTCCCCTCCTCTGAGAGAAGATGACAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatctgccctcatcgtctctcgttgcccacatagatatgtttccatggttcttatagattcttctctatgtttgcag

Basic information

species Zea mays
transcript GRMZM2G179308_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179308_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 2
--GTCAAACAAGAGCAGCCTCATGATGGTTCCCCTCCTCTGAGAGAAGATGACAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaatta---------tctgccctcatcgtctctcgttgc-ccacatagatatgtttccatgg--ttcttatagattcttctctatgtttgcag---------------
  |||  |  | | |  |||| |  || |||||||||||||||||||||||||| |||||| || | ||| |||||||||||||| ||||||||| | || ||||||||         | |   || |     | | | ||   ||  || |  | || | ||    ||  | |  |   || |  |  | | |                 
TCGTCCCAGGAAATC--CCTCGTTTTGCTTCCCCTCCTCTGAGAGAAGATGACAAGGATGGACACTTTGTCTTTGCTGTTGGAGACAACCTCACACCACGATgtaattactgaatacattttaacttaaaacatgtagctgtatcatgtatagtttttcctataatattgctgtgaaccttttttgacatatactttttcaatgtttgcag
















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|76281195|gb|DV020763.1|DV020763
EST:     CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGCAAAAATGGGAGAAGGTCAGTTTGGATGGCCATGTCTTC
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAGGTCAGTTTGGATGGCCATGTCTTC
EST: gi|211248594|gb|FL451517.1|FL451517
EST:     TTGCTGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGCAAAAATGGGAGAAGGTCAGTTTGGATGGCCATGTCTTC
genomic: TTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAGGTCAGTTTGGATGGCCATGTCTTC
EST: gi|211232066|gb|FL290153.1|FL290153
EST:     CAGGKATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGCAAAAATGGGAGAAGGT
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAGGT
EST: gi|211192902|gb|FL091618.1|FL091618
EST:     AGGGGATGGGCATTATGTTTTTGCYGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGCNAAAATGGGAGAAGGTCAGTTTGGATGGCCATGTCTTT
genomic: AGGG-ATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAGGTCAGTTTGGATGGCCATGTCTT-
EST: gi|211230015|gb|FL290150.1|FL290150
EST:     CAGGGATGGGCATTATGTTTT-GCTGTTGGAGATCACCTCACATCTCGCT                         ATAAGATCAATGCAAAAATGGGAG
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAG
EST: gi|211232070|gb|FL290157.1|FL290157
EST:     CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGC
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAACAAGAGCAGCCTCATGATGGTTCCCCTCCTCTGAGAGAAGATGACAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatctgccctcatcgtctctcgttgcccacatagatatgtttccatggttcttatagattcttctctatgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT