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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatatgctcttccgcttctagctttgctaaagtttactgacatgtgttttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG

Basic information

species Zea mays
transcript GRMZM2G037342_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037342_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 5
gtaagttatatgct-----cttccgcttctagctttgctaaagttta------ctgacatgtgttttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
||||||| | | ||     || |    | || |||||  || ||||       || |    || | |  |||||| |||||||||| |||||||||| ||| || ||| |||||||||||||
gtaagttctttcctgctcactccaatctttatctttgtcaatgtttctttttcctaaagcatgatatgactgcagGCTGGACTTCTCAGTGCTTATATCATAAAAAAGCTGTACTTCGGCAG
















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|78119306|gb|DV537690.1|DV537690
EST:     TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTATCT                         TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
genomic: TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
EST: gi|71301742|gb|DR786939.1|DR786939
EST:     TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCT                         TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
genomic: TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
EST: gi|32866161|gb|CF005843.1|CF005843
EST:     TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCT                         TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
genomic: TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
EST: gi|20300970|gb|BQ163913.1|BQ163913
EST:     TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCT                         TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
genomic: TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
EST: gi|71426858|gb|DR807908.1|DR807908
EST:     TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCT                         TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
genomic: TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
EST: gi|18964389|gb|BM660977.1|BM660977
EST:     TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCT                         TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
genomic: TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
EST: gi|149058822|gb|EE156843.2|EE156843
EST:     TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCT                         TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
genomic: TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
EST: gi|76912611|gb|DV164818.1|DV164818
EST:     TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCT                         TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
genomic: TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
EST: gi|149015463|gb|EE045330.2|EE045330
EST:     TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCT                         TCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
genomic: TTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG

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), 47 (downstream exon)
Score: 222

CCAGAACTTTGATCCTGGAAATATCAGCAGTGCCAAATTACTGAACTTCATTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG


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

CCAGAACTTTGATCCTGGAAATATCAGCAGTGCCAAATTACTGAACTTCATTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 106

CCAGAACTTTGATCCTGGAAATATCAGCAGTGCCAAATTACTGAACTTCATTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 131

CCAGAACTTTGATCCTGGAAATATCAGCAGTGCCAAATTACTGAACTTCATTGGCAGTTTCCTTTATCTGTTCGGCTCCAGCACCATTCTTGGAGTAGCTgtaagttata ... ttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctcttccgcttctagctttgctaaagtttactgacatgtgttttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG
                               tactgac  putative branch site (score: 131)
                                         tgttttttct  putative PPT
                        taaagttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatatgctcttccgcttctagctttgctaaagtttactgacatgtgttttttctgcagTCTGGACTTCTTAGTGCTTATACCATTAAGAAGTTGTACTTCGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT