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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_T01
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|13490967|gb|BG517731.1|BG517731
EST:     CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGCAAAAATGGGAGAAG
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAG
EST: gi|211230015|gb|FL290150.1|FL290150
EST:     CAGGGATGGGCATTATGTTTT-GCTGTTGGAGATCACCTCACATCTCGCT                         ATAAGATCAATGCAAAAATGGGAG
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAG
EST: gi|211192902|gb|FL091618.1|FL091618
EST:     AGGGGATGGGCATTATGTTTTTGCYGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGCNAAAATGGGAGAAGGT
genomic: AGGG-ATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAGGT
EST: gi|211232064|gb|FL290151.1|FL290151
EST:     CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGCAAAAATGGGAGAAG
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAG
EST: gi|211232066|gb|FL290153.1|FL290153
EST:     CAGGKATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGCAAAAATGGGAGAAG
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAG
EST: gi|211232068|gb|FL290155.1|FL290155
EST:     CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGCAAAAATGGGGAGAAG
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGG-AGAAG
EST: gi|211232070|gb|FL290157.1|FL290157
EST:     CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCT                         ATAAGATCAATGC
genomic: CAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

GTCAAACAAGAGCAGCCTCATGATGGTTCCCCTCCTCTGAGAGAAGATGACAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 279

GTCAAACAAGAGCAGCCTCATGATGGTTCCCCTCCTCTGAGAGAAGATGACAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 467

GTCAAACAAGAGCAGCCTCATGATGGTTCCCCTCCTCTGAGAGAAGATGACAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

GTCAAACAAGAGCAGCCTCATGATGGTTCCCCTCCTCTGAGAGAAGATGACAGGGATGGGCATTATGTTTTTGCTGTTGGAGATAACCTCACATCTCGCTgtaattatct ... atgtttgcagATAAGATCAATGCAAAAATGGGAGAAG


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