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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctacttctgtttgactgtatatctgttccaatcttcaatagacgaattaacatactgtggtatgtgcggtgtacatgctaaatttttgaacttcaatataatctctctgataaatttatatttgttgtactatgctttcctgattggatacagttggaatgttgtttgctttgcag

Basic information

species Zea mays
transcript GRMZM2G111713_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111713_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g45300.1 (Oryza sativa), 5'ss of exon 10
TATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaag-------ctacttctgtttgactgtatatctgttccaatcttcaatagacg-aattaacatactgtggtatgtgcggtgtacatgctaaatttt-tgaacttcaatataatctctctgataaattta-tatttgttgtactatgctttcctgattggatacagttggaatgttgtttgctttgcag
||||||||||||||| |||| |||||| |||||||||| |||||| ||||||||| ||||||||||||||||  | || ||||||||||||||||||||||||||       ||  || |  |||| ||   ||   ||   |||||  | | | |  | |   ||   ||  ||  ||      | |||  |  | |  | | | ||  | | ||   ||  ||  ||||| | |||| ||| |  || | |  ||||||| ||    |  ||  |||            
TATAAAAAATGAACTGAAGAAAAGACAATCCATGTGGAGTTCTGTTCACTGGGAATTGGTGGAGCCTGCTGTGTGCATAAGAACTTTGAGGGCTCGCATGgtaagttaagatctgattttccttgattgctgattgttttttatcttgtacatatgtgactcggatcaagttatagatgttaaa-atatgtcagctctaataaccatccgtttcattattc--atgcatttaatgtttgctgtccagtgatattatgattggttaactataaaactttgcag---------
















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|88758132|gb|DY542273.1|DY542273
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|32845899|gb|CD985580.1|CD985580
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCACG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|76923556|gb|DV169545.1|DV169545
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|4827723|gb|AI668415.1|AI668415
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|50337822|gb|CO532948.1|CO532948
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|89251080|gb|DY622866.1|DY622866
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGG-CCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACT
EST: gi|37383724|gb|CF628889.1|CF628889
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|148938687|gb|EC883023.2|EC883023
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|18181535|gb|BM382745.1|BM382745
EST:     TGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: TGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|89248722|gb|DY620508.1|DY620508
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|71420007|gb|DR804974.1|DR804974
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
EST: gi|211237149|gb|FL440871.1|FL440871
EST:     GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATG                         ATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT
genomic: GGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTT

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), 46 (downstream exon)
Score: 151

TATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 79

TATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 75

TATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 89

TATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctact ... tgctttgcagATTGGCCTCGATAAGAATGACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAAAAAATGAACTAAAGAGAAGACAGTCCATGTGGAATTCTGTACACTGGGAACTGGTGGAGCCTGCTGTTAGTATCAGAACTTTGAGGGCTCGCATGgtaagctacttctgtttgactgtatatctgttccaatcttcaatagacgaattaacatactgtggtatgtgcggtgtacatgctaaatttttgaacttcaatataatctctctgataaatttatatttgttgtactatgctttcctgattggatacagttggaatgttgtttgctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT