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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGACACCTACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaattcaccatgccgtccgcctttgtgttgcatatgactactacctctgatctctaaagcatgatgttttgacaaaacaaataggcagaaaactg...

Basic information

species Zea mays
transcript GRMZM2G100913_T02
intron # 14
splice site 5'
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|87156257|gb|DY401046.1|DY401046
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGA
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGA
EST: gi|31355723|gb|CD440080.1|CD440080
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|149040127|gb|EE046778.2|EE046778
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|31909111|gb|CD650755.1|CD650755
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|24770194|gb|CA405323.1|CA405323
EST:     CTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: CTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|67010842|gb|CO439591.1|CO439591
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|211250418|gb|FL206019.1|FL206019
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|18173237|gb|BM348625.1|BM348625
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|31364271|gb|CD448626.1|CD448626
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|29543802|gb|CB604182.1|CB604182
EST:     ACAGGGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|30087943|gb|CB886148.1|CB886148
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|31363870|gb|CD448225.1|CD448225
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|211250419|gb|FL206020.1|FL206020
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|31909581|gb|CD650990.1|CD650990
EST:     TGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: TGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
EST: gi|211250420|gb|FL206021.1|FL206021
EST:     ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAG                         CGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT
genomic: ACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 158

AAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGACACCTACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTTGGAGGATGTCCGTGCCACAGGCCAGGCTGCTGGTACATCCAGCACTGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

AAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGACACCTACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTTGGAGGATGTCCGTGCCACAGGCCAGGCTGCTGGTACATCCAGCACTGCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 122

AAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGACACCTACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTTGGAGGATGTCCGTGCCACAGGCCAGGCTGCTGGTACATCCAGCACTGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

AAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGACACCTACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaatt ... tttactgcagCGTGACTCGGAATTACTTTGAGAACCTTGTTCAAGCTTTGGAAGCTGGGTTGGAGGATGTCCGTGCCACAGGCCAGGCTGCTGGTACATCCAGCACTGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGACACCTACAGTGGCTGAATTTGGTGAATTCCGCGTGAAGCTTGCTGGACTTACAAGgtagtaaattcaccatgccgtccgcctttgtgttgcatatgactactacctctgatctctaaagcatgatgttttgacaaaacaaataggcagaaaactg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgtccgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagaaaa