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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcacgccactgctcactagactttttggtggcgcgcctttgccgcatttttcattaatataaggagaatcttgtttttttggggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG

Basic information

species Zea mays
transcript GRMZM2G143602_T03
intron # 7
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|211466861|gb|FL187159.1|FL187159
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCCTGGT-AAAGTTTATGAACGCAGATAACCAGCACC
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCC-TGGTTAAAGTTTATGAACGCAGATAACCAGCACC
EST: gi|21389960|gb|BQ528009.1|BQ528009
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCC
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCC
EST: gi|20507674|gb|BQ279724.1|BQ279724
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGAT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGAT
EST: gi|60348663|gb|DN215636.1|DN215636
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG                         GCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCT

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), 48 (downstream exon)
Score: 420

GTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

GTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 249

GTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 180

GTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacg ... ggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgccgcatttttcattaatataaggagaatcttgtttttttggggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG
              cattaat  putative branch site (score: 180)
 atttttcattaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagcacgccactgctcactagactttttggtggcgcgcctttgccgcatttttcattaatataaggagaatcttgtttttttggggggatgcagGCATAGCAGGAAACCCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT