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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcgcctctgatgctgtcgtgttcatgattccatcgccatcgccgcacttcttaatgatagtagcttatgccgtaacctggagccgggcattgccaactgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTGGAGACGACGATGGTGAACATCCAGGACCTGCCGCTGGAGGCGGTCCTCG

Basic information

species Zea mays
transcript GRMZM2G178102_T01
intron # 16
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|149110139|gb|EE293957.2|EE293957
EST:     CACAGCGACGCGATACTCTGCTGCTCTCTGAAG                         CCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
genomic: CACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
EST: gi|71310371|gb|DR791491.1|DR791491
EST:     TGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAG                         CCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
genomic: TGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
EST: gi|6021905|gb|AW066833.1|AW066833
EST:     GCGACGCGATACTCTGCTGCTCTCTGAAG                         CCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
genomic: GCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
EST: gi|89247875|gb|DY619661.1|DY619661
EST:     ATACTCTGCTGCTCTCTGAAG                         CCGCCGGCTTTCACGCTCAAGTTTGCCAACAGCGCCGGCTTCGACATCCTG
genomic: ATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
EST: gi|78024201|gb|DV492588.1|DV492588
EST:     AAGCACAGCGACGCGATATTCTGCTGCTCTCTGAAG                         CCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTTGACATCCTG
genomic: AAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
EST: gi|148960629|gb|EE011257.2|EE011257
EST:     TGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAG                         CCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTGGACATCCTG
genomic: TGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
EST: gi|60341255|gb|DN208228.1|DN208228
EST:     TGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAG                         CCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
genomic: TGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
EST: gi|148932540|gb|EC876347.2|EC876347
EST:     TGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAG                         CCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG
genomic: TGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTG

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), 48 (downstream exon)
Score: 43

CACTGGAACGGAGATCCGCTGGTCGGACACCGAAGGCGCGGACTCTCCACTGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTGGAGACGACGATGGTGAACATCCAGGACCTGCCGCTGGAGGCGGTCCTCG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 13

CACTGGAACGGAGATCCGCTGGTCGGACACCGAAGGCGCGGACTCTCCACTGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTGGAGACGACGATGGTGAACATCCAGGACCTGCCGCTGGAGGCGGTCCTCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 37

CACTGGAACGGAGATCCGCTGGTCGGACACCGAAGGCGCGGACTCTCCACTGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTGGAGACGACGATGGTGAACATCCAGGACCTGCCGCTGGAGGCGGTCCTCG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 21

CACTGGAACGGAGATCCGCTGGTCGGACACCGAAGGCGCGGACTCTCCACTGATGCTGTTCTGGAAGCACAGCGACGCGATACTCTGCTGCTCTCTGAAGgtcagtcgcc ... ctgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTGGAGACGACGATGGTGAACATCCAGGACCTGCCGCTGGAGGCGGTCCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgatagtagcttatgccgtaacctggagccgggcattgccaactgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTGGAGACGACGATGGTGAACATCCAGGACCTGCCGCTGGAGGCGGTCCTCG
                  ccgtaac  putative branch site (score: 21)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtcgcctctgatgctgtcgtgttcatgattccatcgccatcgccgcacttcttaatgatagtagcttatgccgtaacctggagccgggcattgccaactgcttgcagCCGCCGGCTTTCACGCTCAAGTTCGCCAACAGCGCCGGCTTCGACATCCTGGAGACGACGATGGTGAACATCCAGGACCTGCCGCTGGAGGCGGTCCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG