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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtttgttctgtattagtgtgtttttgtttcacgtgaattcactagattagtctactgttgccaattggattagaacgtaaaccaagtccaatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT

Basic information

species Zea mays
transcript GRMZM2G032367_T04
intron # 1
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|91048787|gb|EB159205.1|EB159205
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|148953376|gb|EE152870.2|EE152870
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|6127287|gb|AW129812.1|AW129812
EST:     CTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CTCCCCGCGCCGCCGTTCGCCGAAG--CC-C--CGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|30705068|gb|CD058657.1|CD058657
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGGAAGGAAAAT
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCT-GAA-GAGAAT
EST: gi|101393982|gb|EB818924.1|EB818924
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|88757330|gb|DY541471.1|DY541471
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTT
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|91878167|gb|EB408124.1|EB408124
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|32907328|gb|CF012141.1|CF012141
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTCG                         C
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcag-
EST: gi|32907328|gb|CF012141.1|CF012141
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTCG                         C
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcag-
EST: gi|91048031|gb|EB158449.1|EB158449
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|60359697|gb|DN226670.1|DN226670
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|76020657|gb|DT947827.1|DT947827
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|71327453|gb|DR800341.1|DR800341
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|71448913|gb|DR829963.1|DR829963
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|50338207|gb|CO533333.1|CO533333
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|149084255|gb|EE173682.2|EE173682
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|149110785|gb|EE190606.2|EE190606
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAG                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
EST: gi|37420962|gb|CF648177.1|CF648177
EST:     CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAA                         AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC
genomic: CCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 269

AAAGCCCATCTCACAGCCCCGCAGCCTCTTCTCCTCGTCCATCTCTTCCGCCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 545

AAAGCCCATCTCACAGCCCCGCAGCCTCTTCTCCTCGTCCATCTCTTCCGCCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 525

AAAGCCCATCTCACAGCCCCGCAGCCTCTTCTCCTCGTCCATCTCTTCCGCCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 532

AAAGCCCATCTCACAGCCCCGCAGCCTCTTCTCCTCGTCCATCTCTTCCGCCTCCCTCCCCGCGCCGCCGTTCGCCGAAGCCCCGCGTCGCGTCGCGTAGgtaacttcta ... caatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattagtctactgttgccaattggattagaacgtaaaccaagtccaatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT
                         attagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtttgttctgtattagtgtgtttttgtttcacgtgaattcactagattagtctactgttgccaattggattagaacgtaaaccaagtccaatttgcagAGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA