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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtgaagtacacctatctttcatataattgaaaagtgattattttttctgaggcactaggtattagcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT

Basic information

species Zea mays
transcript GRMZM2G109677_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 4
----------------------------gagtgaagtacacctatct-ttcatataattgaaaagtgattattttttctgaggcactaggtattagcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
                              ||    |   ||  ||| ||||  |||||| |  || |  || |  | | |         | || |   | || | |  ||  | ||| | |  || |||||||||| |||||||| ||||||||||||||||||||||| |||||||| ||| ||||||||||||||||||| || |||||||||||||| ||||| |
gtcagtaacctactgttattttactatcttgtattttgagcccttctattcagttaattggatggtaaccatgtgctgtaaat-------tgtttgttcattctcattctaaatctttatgtgcttcagATTAGGAAAATGAAGGGCTTGAAGCAGAAGAAGGCTCACCTCATGGAGATCCAGATCAATGGTGGTACCATTGCCGATAAGGTGGACTATGGATACAAGT

upper sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G30810.1 (Glycine max), 3'ss of exon 4
gagtgaagtacacctatctttcatataattgaaaagtgattattttttctgagg-cactaggtattagcaaactc---acctcttatgta-tttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
        |  |  |    ||  |  ||||  ||| | |   |  || | |    |||  | | |    | | ||   |   | | | |   ||  |||||  |||| ||||| ||||| || |||||||||||||| || ||  | ||||| |||||||| ||||||||||| |||||  | |||||||||| ||  ||||  |
-----ccttctattttgtgtttgtcaaattccaaattcagagtccttccagttatcacatgatttagatatattcctaatagcctgtctggcttaaatcttacagATCAGGAAAATGAAAGGGTTGAAGCAGAAGAAAGCCCATATCATGGAAATTCAGGTTAATGGTGGTACTATTGCACAGAAGGTGGACTTTGCATACAGTT

upper sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G36780.1 (Glycine max), 3'ss of exon 4
gagtgaagtacacctatctttcatataattgaaa-----agtgattattttttctgaggcactaggtattagcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
   | | || |   ||  |   |  |||  |  |     | | || |    || | | |    || | |   |  | |   || |  ||   ||| |||||  |||| ||||| ||||| || |||||||||||||| || ||  | ||||| |||||||| ||||||||||  |||||  | |||||||||| ||  ||||  |
---ttatgttcttttaattccaaattaagagtcacttccaattatcacaaattatcatgattgagatttattcctaatagtctgtc-tgc-cttgaatcttacagATCAGGAAAATGAAAGGGTTGAAGCAGAAGAAAGCCCATATCATGGAAATTCAGGTTAATGGTGGTAGTATTGCACAAAAGGTGGACTTTGCATACAGTT

upper sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT1G43170.7 (Arabidopsis thaliana), 3'ss of exon 4
gagtgaagtacacctatctttcatataattgaaaagtg-attattttttctgaggcactaggtattagcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
       |||    |   |   ||  ||| |||  ||  || ||    |||   |||||| ||  |  |  ||     |  |||||         ||  |||| |||||||||||||| ||||||||||||||||||||| |||||||||| ||| |||||||||||||||||||  | ||||| |||| || |||||  |
-------gtaagtttgctt---attgaatggaagtgtatatcataaactcttctgcactacgttcttactgac---aattctatgtgacctctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATCCAGATCAATGGTGGTACCATTGCCCAGAAGGTTGACTTTGCCTACAGTT

upper sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
gagtgaagtacacctatctttcatataattgaaaagtgattattttttctgaggcactaggtattagcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
                | |  ||| || || |||  | |  ||  |||   |      |  | ||    |   |   | ||   |||       |||||||| ||||| ||||| ||  |||||||||||||||| || ||||  ||||||||| ||||||||||    || ||  | || || ||||||| || ||  |
---------------gtatgccatttacttcaaat-tcacaatcattttgcaaatttcatttgtttctgattacgattgttggatat------gttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT

upper sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0072g00340.t01 (Vitis vinifera), 3'ss of exon 4
--gagtgaagtacacctatctttcatataattgaaa-agtgattattttttctgaggcactaggtattagcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
     ||| |     | ||  |||| |   | |    ||   | || |   || |   |     |||   | |||| |  |||   ||  | || |  | |||||||||||||||||||| |||||||||||||| || ||| |||||||||| |||||||||||||| ||||||||| | || ||||| ||||  ||    |
ttatttgacgcttgtcaatacttcaaaatttagttccagctctcatatcccctaaatgatcct-tatcctctaactaatttctctggtcatggtgt--tatagATTAGGAAGATGAAGGGATTGAAGCAGAAGAAAGCACACTTGATGGAGATCCAGGTCAATGGTGGAACCATTGCTCAGAAAGTGGATTATGCTTATGGTT

upper sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0035g01020.t01 (Vitis vinifera), 3'ss of exon 3
--------gagtgaagtacacctatctttcatataattgaaaagtgattattttttctg--aggcactaggtatt-agcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
           | |   | |  |    |||| | | || |    | |   || |   ||  ||  || |  ||||  |||    ||  || ||| |         || |||||||| || ||||||||  |||||||||| ||||||||||| |||||||||||||| ||||||||     ||||| | ||||| ||||||| |||    |
gtagttttccatcaccaatatttgggattcaaagactttaggtttcacatttataaatgcaagttaccaattatttggcactgacatatcctatatggaatggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATTCAGGTGAATGGTGGAGATGTTGCTAAGAAGGTTGACTATGCCTATGGTT

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|32912719|gb|CF017531.1|CF017531
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCGCCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|9953363|gb|BE639946.1|BE639946
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|31611943|gb|CD568565.1|CD568565
EST:     GAAGAAATATGCTTCTG-TATCCGTGTCATTGCTCATACCCAG                         ATTA-GAAGATGAAGGG-TTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: GAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211226039|gb|FL295893.1|FL295893
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|67028663|gb|CO457412.1|CO457412
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|31355515|gb|CD439872.1|CD439872
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|33093760|gb|CF053754.1|CF053754
EST:     GAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCGCCTGATGGAGATT
genomic: GAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|5268598|gb|AI770562.1|AI770562
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGAT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGAT
EST: gi|67023430|gb|CO452179.1|CO452179
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|67018173|gb|CO446922.1|CO446922
EST:     TGAAGAAAT-TGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: TGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|15313062|gb|BI478539.1|BI478539
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|32912720|gb|CF017532.1|CF017532
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCGCCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211256710|gb|FL283521.1|FL283521
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGNGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAKAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|5268417|gb|AI770381.1|AI770381
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|22521166|gb|BU079977.1|BU079977
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|32930935|gb|CF035747.1|CF035747
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|26557715|gb|CA829950.1|CA829950
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|33100628|gb|CF060588.1|CF060588
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|22545506|gb|BU097865.1|BU097865
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211223173|gb|FL365205.1|FL365205
EST:     GTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: GTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211256712|gb|FL283523.1|FL283523
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|6637012|gb|AW261284.1|AW261284
EST:     AGAAGATGAAGAAATATGTTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGNTTGAAGCAGAAGAAGGCTCTCCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|24765393|gb|CA400552.1|CA400552
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgaggcactaggtattagcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
                        aactcac  putative branch site (score: 2)
                                             tatctttt  putative PPT
                                       tatttgtatctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtgaagtacacctatctttcatataattgaaaagtgattattttttctgaggcactaggtattagcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA