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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaaagcaaaccctcctgtgccctgccccgactcttgttttccactgctggttttactttgtggatcccaaaccttactggtcccgtccatttgaaattggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGCAGTCAGCAGGGAAATCTCATCGTCGTTGGGCCTAACCGGGCTTTGCTGC

Basic information

species Zea mays
transcript GRMZM2G162284_T02
intron # 7
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|22472639|gb|BU037119.1|BU037119
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|67041980|gb|CO468235.1|CO468235
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|24767005|gb|CA402150.1|CA402150
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|31359518|gb|CD443875.1|CD443875
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|67015235|gb|CO443984.1|CO443984
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|14203924|gb|BG837601.1|BG837601
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|26558436|gb|CA830671.1|CA830671
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|21891488|gb|BQ744701.1|BQ744701
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|211010348|gb|FL233634.1|FL233634
EST:     TGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGSACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTG
genomic: TGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGG-ACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTG
EST: gi|28984233|gb|BQ539002.2|BQ539002
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|71436984|gb|DR818034.1|DR818034
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|211010351|gb|FL233637.1|FL233637
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|211010356|gb|FL233642.1|FL233642
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|4874486|gb|AI674006.1|AI674006
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|78112438|gb|DV530832.1|DV530832
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|211159313|gb|FL469871.1|FL469871
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTKATGAGTGATGGATGACGGGTGAAACTYTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|87155374|gb|DY400163.1|DY400163
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
EST: gi|21828650|gb|BQ703334.1|BQ703334
EST:     CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG                         GGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC
genomic: CTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGC

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), 49 (downstream exon)
Score: 60

TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGCAGTCAGCAGGGAAATCTCATCGTCGTTGGGCCTAACCGGGCTTTGCTGC


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 21

TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGCAGTCAGCAGGGAAATCTCATCGTCGTTGGGCCTAACCGGGCTTTGCTGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 35

TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGCAGTCAGCAGGGAAATCTCATCGTCGTTGGGCCTAACCGGGCTTTGCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAGgtcaaagcaa ... ggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGCAGTCAGCAGGGAAATCTCATCGTCGTTGGGCCTAACCGGGCTTTGCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttgtggatcccaaaccttactggtcccgtccatttgaaattggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGCAGTCAGCAGGGAAATCTCATCGTCGTTGGGCCTAACCGGGCTTTGCTGC
                 accttac  putative branch site (score: 78)
                                   atttgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaaagcaaaccctcctgtgccctgccccgactcttgttttccactgctggttttactttgtggatcccaaaccttactggtcccgtccatttgaaattggttttgcagGGTGATGAGTGATGGATGACGGGTGAAACTCTGGGCTGCCCAAGTGCTTGCAGTCAGCAGGGAAATCTCATCGTCGTTGGGCCTAACCGGGCTTTGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC