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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgtggttaaaaataccgaccacgtgcgtacagggagggtcttattatacccaaatccgatccgtggtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCGTAGGCGTAGCTGCGGCGGCGGGTACGTGAAGGTGAAGCTGGAAGGGGTG

Basic information

species Zea mays
transcript GRMZM2G000158_T02
intron # 1
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|211107898|gb|FL115286.1|FL115286
EST:     GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         TGTACCCAGGAATGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGC
genomic: GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAA-GAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGC
EST: gi|7844083|gb|AW787286.1|AW787286
EST:     GTCGTCGACCATGAACAGCAAAGCAACAA                         TGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: GTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
EST: gi|74234745|gb|DT642659.1|DT642659
EST:     GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         -G-A---AG-AAGA-G-G-CTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
EST: gi|7844084|gb|AW787287.1|AW787287
EST:     ACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         TGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: ACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
EST: gi|211108803|gb|FL115290.1|FL115290
EST:     GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         TGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
EST: gi|211108802|gb|FL115289.1|FL115289
EST:     GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         TGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
EST: gi|211119373|gb|FL414335.1|FL414335
EST:     GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         -G-A---AG-AAGA-G-G-CTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
EST: gi|78081855|gb|DV510267.1|DV510267
EST:     GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         TGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
EST: gi|71448007|gb|DR829057.1|DR829057
EST:     GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         TGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
EST: gi|78179144|gb|DV549517.1|DV549517
EST:     GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         TGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
EST: gi|211108800|gb|FL115287.1|FL115287
EST:     GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAA                         TGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG
genomic: GGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCG

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: 46 (upstream exon), 49 (downstream exon)
Score: 10

AGGCGGCCACGCTTCCGCTCTTCGTCTGCGAGGATGGCGACGGAGGCGGCGGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCGTAGGCGTAGCTGCGGCGGCGGGTACGTGAAGGTGAAGCTGGAAGGGGTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 17

AGGCGGCCACGCTTCCGCTCTTCGTCTGCGAGGATGGCGACGGAGGCGGCGGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCGTAGGCGTAGCTGCGGCGGCGGGTACGTGAAGGTGAAGCTGGAAGGGGTG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 6

AGGCGGCCACGCTTCCGCTCTTCGTCTGCGAGGATGGCGACGGAGGCGGCGGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCGTAGGCGTAGCTGCGGCGGCGGGTACGTGAAGGTGAAGCTGGAAGGGGTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 46

AGGCGGCCACGCTTCCGCTCTTCGTCTGCGAGGATGGCGACGGAGGCGGCGGCGACCGCGACCGCGACGGCGTCGTCGACCATGAACAGCAAAGCAACAAgtgagttgtg ... gtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCGTAGGCGTAGCTGCGGCGGCGGGTACGTGAAGGTGAAGCTGGAAGGGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgtgcgtacagggagggtcttattatacccaaatccgatccgtggtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCGTAGGCGTAGCTGCGGCGGCGGGTACGTGAAGGTGAAGCTGGAAGGGGTG
                  tcttattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgtggttaaaaataccgaccacgtgcgtacagggagggtcttattatacccaaatccgatccgtggtgtgtgtagTGTACCCAGGAAGAAGAGGCTGGTGGGGTGGCCGCCGGTGAAGTGCGCGCGTAGGCGTAGCTGCGGCGGCGGGTACGTGAAGGTGAAGCTGGAAGGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG