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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGTTTTGGCGGAAGGCAATGCTGGCTCAGGACCATCTACTACCGGCCTTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccggaccttgttaatcagtgtttatgtccgaaaccgatgctgcttgcttgcctcactcagatgattcatatgagcacctatggaaatgaaatg...

Basic information

species Zea mays
transcript GRMZM2G115372_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115372_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os03g63500.2 (Oryza sativa), 5'ss of exon 12
GGATGTTTTGGCGGAAGGCAATGCTGGCTCAGGACCATCTACTACCGGCCTTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccggaccttgttaatcagtgtttatgtccgaaaccgatgctgcttgcttgcctcactcagatgattcatatgagcacctatggaaatgaaatg-------
||||||||| || ||||| |||| |||  |||  || ||| |||| ||||| ||||| || |||||||| ||||||||||||||||| ||||| ||||||||| |||     | || ||| |   || || |  |   |   | |   | |     ||   | | |  |       || ||||| |  |||  |||| |        
GGATGTTTTAGCAGAAGGTAATGTTGGTGCAGCGCCTTCTCCTACAGGCCTAGTGGCAATTTTGTCTGGCCAAGAAGAGATGTTTGCATTCCGTAGGGCGgtaagtaaatagcatttttactttctgattgtagct--acttgcttgagttcaaacgcactagtgaagtatc----attagcac-tggggagttgaatttcgttcag
















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|149088177|gb|EE287320.2|EE287320
EST:     TTGTGGGGATATTGTTTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCACGGCTTATCGAGATGCAGACCCCGCTGTATTTGGAGCGTGTGCTG
genomic: TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG
EST: gi|166483025|gb|EG161620.1|EG161620
EST:     TGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCACGGCTTATCGAGATGCAGACCCCGNTGTATCTGGAGC
genomic: TGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGC
EST: gi|32844278|gb|CD983959.1|CD983959
EST:     TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCAG
genomic: TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG
EST: gi|16926163|gb|BM079231.1|BM079231
EST:     TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG
genomic: TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG
EST: gi|78076776|gb|DV505210.1|DV505210
EST:     TTGTGGCGATATTGTTTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCACGGCTTATCGAGATGCAGACCCCGCTGTATTTGGAGGGTGTGCTG
genomic: TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG
EST: gi|32845460|gb|CD985141.1|CD985141
EST:     TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCAG
genomic: TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG
EST: gi|32836721|gb|CD976399.1|CD976399
EST:     TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCAG
genomic: TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG
EST: gi|32844915|gb|CD984596.1|CD984596
EST:     TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCCCGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCAG
genomic: TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG
EST: gi|32844695|gb|CD984376.1|CD984376
EST:     TGTGGCGATATTGTTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCCCGGCTTATCGAGATGCAGACNCCGCTGTATCTGGAGCGTGTGCAG
genomic: TGTGGCGATATTGT-CTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG
EST: gi|83278407|gb|DV942415.1|DV942415
EST:     TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCG                         ATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCAG
genomic: TTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTG

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 2 RNA-Seq libraries.


Block sizes: 24 (upstream exon), 46 (downstream exon)
Score: 5

GGATGTTTTGGCGGAAGGCAATGCTGGCTCAGGACCATCTACTACCGGCCTTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTGGCTGTACATCCCTCGTTCCGTCGTCCTGGTCTTGCAAGAAATAACAGGC


Block sizes: 24 (upstream exon), 46 (downstream exon)
Score: 7

GGATGTTTTGGCGGAAGGCAATGCTGGCTCAGGACCATCTACTACCGGCCTTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccg ... tgttttgcagATATCACGGCTTATCGAGATGCAGACCCCGCTGTATCTGGAGCGTGTGCTGGCTGTACATCCCTCGTTCCGTCGTCCTGGTCTTGCAAGAAATAACAGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGTTTTGGCGGAAGGCAATGCTGGCTCAGGACCATCTACTACCGGCCTTGTGGCGATATTGTCTGGTCAAGAAGAGATGTTTGCGTTCCGCAGGGCGgtatgtaccggaccttgttaatcagtgtttatgtccgaaaccgatgctgcttgcttgcctcactcagatgattcatatgagcacctatggaaatgaaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaatgaa