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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatgcaagtgaagtatgcaggtttatccactaaaatattttacatatgcacatatggatcatatttgcacttttgacattctctaatcttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG

Basic information

species Zea mays
transcript GRMZM2G180815_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g44394.1 (Oryza sativa), 3'ss of exon 5
----tttcatgcaagtgaagtatgcaggtttatccactaaaatattttacatatgcacatatggatcatatttgcacttttgacattctctaatcttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG
     | ||  ||  | || | |    ||||||| |||  ||   |  |||  |  | || |   |   |  |   |   ||||  | ||  ||  |  || ||||||||||||||||||||  ||||||||| || ||||||||||||||||||||||||||||||||||| ||||| ||| ||
ctctctacaaccagttcaaatttctgtgtttatc-actgtaacgctggacactt-taaatgtcatttgcaagt-tgcaactgacgct-tccgatgcttcaacagGCTGAATTCAAGAGGATTGTGTCACCTTTAAAACTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAGCAAGGGTTTCTG

upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G05740.1 (Glycine max), 3'ss of exon 5
tttcatgcaagtgaagtatgcaggtttatccactaaaatattttacatatgcacatatggatca-tatttgc-acttttgacattctctaatcttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG
 | ||| ||     | ||| ||  | | |  | |   || || |    ||    || |    || | | | | || ||| ||  |   | || ||   | ||| |||||||||||| |||   ||||| ||||||   || |||||||| ||||||||||| ||||| ||||||||||| |||
atacattcataaacaatattcat-tctgttgatttttattttcttttcatttctatttttgccagtgtctcctacattttaccattgttcat-ttgctacagGTTGAATTCAAGAGAATTGTTTCACCCTTGAAGTATCAAACAAGGTGCCTTGCTGCATTCCCTGACCAACAAGGTTTCTTG

upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 5
tttcatgcaagtgaagtatgcaggtttatccactaaaatattttacatatgcacatatggatca-tatttgc-acttttgacattctctaatcttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG
 | |||  |     | ||| ||  | | |  | |    | || |    ||     |||     | | | | | || ||||||  |   | || ||   | ||| |||||||||||| |||   ||||| || |||   || |||||||| ||||||||||| ||||||||||||||||| |||
atacattaataaacaatattcat-tctgttgatttttcttttcttttcatttctgtatttgctagtgtctcctacctttgaccattgttcat-ttgctacagGTTGAATTCAAGAGAATTGTTTCACCATTAAAGTATCAAACAAGGTGCCTTGCTGCATTCCCTGATCAACAAGGTTTCTTG

upper sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 5
tttcatgcaagtgaagtatgcaggtttatccactaaaatattttacat-atgcacatatggatcatatt----tgcacttttgacattctctaatcttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG
         ||| ||| ||   | | | || || |  || ||  |||  ||  ||   |   | |||||    | || || | | | |   | |  |   || || | || || ||||| || || |||||  |||||   |||||||| ||| |||| |||||||||||||| |||||||| || 
----gattgagtcaaggatctggttctttctaccatcat-ttgcacaccatttactagttctttatattctacttcaattctaataattatttaaataccaacagACCGAGTTTAAGAGAATCACTTCACCCCTGAAGTATCAGACAAGATGTGTTGCAGCATTTCCTGATCAGCAAGGTTTCTTA

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|50331331|gb|CO526457.1|CO526457
EST:     TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|84969286|gb|DW467729.1|DW467729
EST:     CAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: CAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|71448754|gb|DR829804.1|DR829804
EST:     TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|78073885|gb|DV502319.1|DV502319
EST:     TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|71758084|gb|DR956021.1|DR956021
EST:     CAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: CAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|74234227|gb|DT642141.1|DT642141
EST:     TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|71432894|gb|DR813944.1|DR813944
EST:     TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|50332450|gb|CO527576.1|CO527576
EST:     TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|29543837|gb|CB604217.1|CB604217
EST:     TGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCNCAG                         GCTGAATTCAAGAGGATTACGTCNCCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|74240564|gb|DT648478.1|DT648478
EST:     TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|76930213|gb|DV172299.1|DV172299
EST:     TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
EST: gi|76286199|gb|DV025767.1|DV025767
EST:     TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAG                         GCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT
genomic: TTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTT

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: 79

ACTTCCTGAGCGTTGCTATGCTCTATCGCTTTGTTATCCTCTCATGGTGGTTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 12

ACTTCCTGAGCGTTGCTATGCTCTATCGCTTTGTTATCCTCTCATGGTGGTTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 18

ACTTCCTGAGCGTTGCTATGCTCTATCGCTTTGTTATCCTCTCATGGTGGTTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 32

ACTTCCTGAGCGTTGCTATGCTCTATCGCTTTGTTATCCTCTCATGGTGGTTGGCACTGCTGATCGCAACGTAATAGTCTTCAATCTGCAGAATCCACAGgtaatattgc ... cttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgcacatatggatcatatttgcacttttgacattctctaatcttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG
                                      ctctaat  putative branch site (score: 32)
                                       tctaatcttataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcatgcaagtgaagtatgcaggtttatccactaaaatattttacatatgcacatatggatcatatttgcacttttgacattctctaatcttataaaagGCTGAATTCAAGAGGATTACGTCACCTTTGAAGCTCCAGACAAGGTGTCTTGCTGCATTTCCTGATCAACAAGGTTTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
-ttcatgc
- - - - - - - -gtatgca
- - - - - - - - - - - - - - - - - - - - - - - -tatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcactt