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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccatttctaaaccctgatgtctttcttgaggtcaacacttgaaattcttagtgttaattaacttgctgtttatcttgtatattttcttaacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTCTCTGGAGGGCTTCATGGTGTTGGCTTATCAGTTGTTAATGCTTTATCAG

Basic information

species Zea mays
transcript GRMZM2G111014_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111014_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 5
tgccatttctaaaccctgatgtctttcttgaggtcaa--cacttgaaattcttagtgttaattaacttgctgtttatcttgtatattttcttaacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTCTCTGGAGGGCTTCATGGTGTTGGCTTATCAGTTGTTAATGCTTTATCAG
   | ||   |||  |  || | |        ||  |  || |||  || |  |||||| |  |  |||      |     | || ||| ||||| ||||||||||||||||||||||||||||||||||||||||| ||||| |||| ||| ||||||||||| |||||||||||| ||||||||||||||||||| ||||
--accttctaaaaaacaaatatgtgcgacattgtttatccatttggcatacccagtgttcaacatgttggatgccaatcaatctaattttttaaccatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAGAGTGGCTACACTGTTTCTGGAGGGCTGCATGGTGTTGGCCTATCAGTTGTTAATGCTTTGTCAG

upper sequence: GRMZM2G111014_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 5
tgccatttctaa---accctgatgtctttcttgag-gtcaacacttgaaattcttagtgttaattaacttgctgtttatcttgtatattttcttaacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTCTCTGGAGGGCTTCATGGTGTTGGCTTATCAGTTGTTAATGCTTTATCAG
   |||||  ||         ||  |  | |||    | || || ||   || ||  | ||  ||   |||      ||  | |||  |     ||   ||||| |  | || || |||||||||||||| ||| | |  |||||||| ||||| ||||| || || |||||||| |||||||| ||||||||||| || ||||
--gcattttcaatgtgtttcaataccaatattgcttattaagacatgt--tttttttttttttttcttttgtgcaaaattatttatgatcaacaaaatctgcagGTCTTACATGCAGGTGGCAAATTTGGTGGTGCCAGCAGTGGTTATAGTGTATCTGGTGGACTACATGGTGTGGGCTTATCTGTTGTTAATGCCTTGTCAG
















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|32924684|gb|CF029496.1|CF029496
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32926908|gb|CF031720.1|CF031720
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGGGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|31612357|gb|CD568979.1|CD568979
EST:     ATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: ATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925623|gb|CF030435.1|CF030435
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925026|gb|CF029838.1|CF029838
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925749|gb|CF030561.1|CF030561
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925219|gb|CF030031.1|CF030031
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925064|gb|CF029876.1|CF029876
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|5268379|gb|AI770343.1|AI770343
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAGAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925570|gb|CF030382.1|CF030382
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925327|gb|CF030139.1|CF030139
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925639|gb|CF030451.1|CF030451
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925015|gb|CF029827.1|CF029827
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32924772|gb|CF029584.1|CF029584
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925454|gb|CF030266.1|CF030266
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32926273|gb|CF031085.1|CF031085
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925309|gb|CF030121.1|CF030121
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925339|gb|CF030151.1|CF030151
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
EST: gi|32925242|gb|CF030054.1|CF030054
EST:     CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACA                         TTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC
genomic: CTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTC

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), 44 (downstream exon)
Score: 138

ATTCCTACTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTCTCTGGAGGGCTTCATGGTGTTGGCTTATCAGTTGTTAATGCTTTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

ATTCCTACTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTCTCTGGAGGGCTTCATGGTGTTGGCTTATCAGTTGTTAATGCTTTATCAG


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 24

ATTCCTACTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTCTCTGGAGGGCTTCATGGTGTTGGCTTATCAGTTGTTAATGCTTTATCAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 42

ATTCCTACTGATATGCACCCCCAGACGAAGAAATCTTGTGTGGAGACTGTCTTAACAgtatggttaa ... aacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTCTCTGGAGGGCTTCATGGTGTTGGCTTATCAGTTGTTAATGCTTTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttagtgttaattaacttgctgtttatcttgtatattttcttaacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTCTCTGGAGGGCTTCATGGTGTTGGCTTATCAGTTGTTAATGCTTTATCAG
                                         tcttaac  putative branch site (score: 42)
                                      ttttctta  CT-rich tract
                         tttatcttgtatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccatttctaaaccctgatgtctttcttgaggtcaacacttgaaattcttagtgttaattaacttgctgtttatcttgtatattttcttaacgatgcagTTAATGCACGCTGGTGGCAAATTTGGAGGTTCAAAAAGTGGTTACAGTGTCTCTGGAGGGCTTCATGGTGTTGGCTTATCAGTTGTTAATGCTTTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
tgccatt
- - - - - - - cctgatg
- - - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt