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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggattacgcattgtgttgtgttgtgttgccatcagcaggtcctacagatcctggacaggtcctagctagctgctaactatatatgtatcggcgaatgaaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGCAACCGG

Basic information

species Zea mays
transcript GRMZM2G079127_T01
intron # 3
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|211379542|gb|FL395180.1|FL395180
EST:     CTGGGTACATKAAGAACGCAGARGGTTGCGCTGGACGCCCTCTCAATATG                         CCTCAACATCAAACGGCTGGGAGATGATGATTTCCATCGGC
genomic: CTGGGTACATGAAGAACGCAGA-GGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAA-CGGCTGGGAGATGATGATTTCCATCGGC
EST: gi|29544383|gb|CB604763.1|CB604763
EST:     ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATG                         CCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGC
genomic: ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGC
EST: gi|211133233|gb|FL429632.1|FL429632
EST:     ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATG                         CCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGG
genomic: ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGG
EST: gi|89760889|gb|DY689119.1|DY689119
EST:     ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATG                         CCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGC
genomic: ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGC
EST: gi|148944005|gb|EC889088.2|EC889088
EST:     GCAGAGGTTGCGCTGGACGCCCTCTCAATATG                         CCTCAACATCAACGGCTGGGAGATGATGA-TTCCATCGGCTTTCTGGCGGC
genomic: GCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGC
EST: gi|211046130|gb|FL426055.1|FL426055
EST:     ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATG                         CCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTG
genomic: ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTG
EST: gi|29946165|gb|CB816012.1|CB816012
EST:     ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATG                         CCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGC
genomic: ACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGC

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), 46 (downstream exon)
Score: 64

TTTGGAGCTGTGGTACAACACCATACTGGTGCTGCTCACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGCAACCGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 55

TTTGGAGCTGTGGTACAACACCATACTGGTGCTGCTCACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGCAACCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 16

TTTGGAGCTGTGGTACAACACCATACTGGTGCTGCTCACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGCAACCGG


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 25

TTTGGAGCTGTGGTACAACACCATACTGGTGCTGCTCACTGGGTACATGAAGAACGCAGAGGTTGCGCTGGACGCCCTCTCAATATGgtagggatta ... aaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGCAACCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacaggtcctagctagctgctaactatatatgtatcggcgaatgaaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGCAACCGG
                  tgctaac  putative branch site (score: 25)
                     taactatatatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggattacgcattgtgttgtgttgtgttgccatcagcaggtcctacagatcctggacaggtcctagctagctgctaactatatatgtatcggcgaatgaaacgtgcagCCTCAACATCAACGGCTGGGAGATGATGATTTCCATCGGCTTTCTGGCGGCAACCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG