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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataattgaattttgggctgcacaagtttttgcaagcatgacagacattcttatctgtttcttgggatatttggtgtcatttttaataatccttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG

Basic information

species Zea mays
transcript GRMZM2G341404_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g10180.2 (Oryza sativa), 3'ss of exon 7
ataattgaattttgggctgcacaagtt--tttgcaagcatgac-agacatt-cttatctgtttcttgggatatttggtgtcatttttaataatccttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG
    ||        | |    ||| |   || |     ||  | |||  |  ||  ||| || |||    |  ||| ||| || ||   |  | || | ||||||||||||||||||| |||||  ||||||| ||||||||||| ||||||||| |||||||||| |||||||||||||| |||
---gttatgcaccagacaatgcaattgaattagttgttatagccagatctcgctagtctcttacttcatctgcttgttgt-atgttaccttctactggttgcagAGAGGTGAAGCTAAGCTTCTTACAGAAGACTGGGAAGGAGCGGTTCAGGATCTAAAAGAGGCTGCCCAGAAATCTCCCCAG

upper sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g74580.2 (Oryza sativa), 3'ss of exon 6
ataattgaattttgggctgcacaagtt--tttgcaagcatgac-agacatt-cttatctgtttcttgggatatttggtgtcatttttaataatccttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG
    ||        | |    ||| |   || |     ||  | |||  |  ||  |||||| |||    |  ||| ||| || ||   |  | || | ||||||||||||||||||| |||||  ||||||| ||||||||||| ||||||||| ||||||| ||  ||||||||||||| |||
---gttatgcaccagacaatgcaattgaattagttgttatagccagatctcactagtctgttacttcatctgcttgttgt-atgttaccttctactggttgcagAGAGGTGAAGCTAAGCTTCTTACAGAAGACTGGGAAGGAGCGGTTCAGGATCTAAAAGAAGCTTCCCAGAAATCTCCCCAG
















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|60394505|gb|DN227375.1|DN227375
EST:     AAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: AAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|19770415|gb|BQ035136.1|BQ035136
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|26456221|gb|CA827804.1|CA827804
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|71323580|gb|DR798458.1|DR798458
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32791567|gb|CD943803.1|CD943803
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|78104564|gb|DV522982.1|DV522982
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTGCACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32805133|gb|CD957369.1|CD957369
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGA
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGA
EST: gi|7227648|gb|AW566289.1|AW566289
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGA
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGA
EST: gi|32799442|gb|CD951678.1|CD951678
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|78080723|gb|DV509135.1|DV509135
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGCAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|91875153|gb|EB405110.1|EB405110
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32796833|gb|CD949069.1|CD949069
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGGT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|26456078|gb|CA827661.1|CA827661
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32799460|gb|CD951696.1|CD951696
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32799713|gb|CD951949.1|CD951949
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|67016841|gb|CO445590.1|CO445590
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGNGAANGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT

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), 49 (downstream exon)
Score: 245

GTGTAAAACTCTGGTTAGACTTGGGAGAAGTAAGGAGGCAATCAGCACTTGTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 354

GTGTAAAACTCTGGTTAGACTTGGGAGAAGTAAGGAGGCAATCAGCACTTGTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 239

GTGTAAAACTCTGGTTAGACTTGGGAGAAGTAAGGAGGCAATCAGCACTTGTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 495

GTGTAAAACTCTGGTTAGACTTGGGAGAAGTAAGGAGGCAATCAGCACTTGTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttatctgtttcttgggatatttggtgtcatttttaataatccttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG
                                  ttttaat  putative branch site (score: 495)
                                           tccttgct  putative PPT
                            tgtcatttttaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataattgaattttgggctgcacaagtttttgcaagcatgacagacattcttatctgtttcttgggatatttggtgtcatttttaataatccttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - -gctgcac
- - - - - - - - - - - - - - -tgcaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttggtg