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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctaaccgcctacctaagtttgtcttttaccatcctgtatgtgcaaaccattgcataaatctgtttgctaattttgttatactacatctgttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG

Basic information

species Zea mays
transcript GRMZM2G156734_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
--gtctaaccgcctacctaagtttgtcttttaccatcctgtatgtgcaaaccattgcataaatctgtttgctaattttgttatactacatctgttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG
   |  || |   ||      ||| | ||||    | |||||| |       |   |||   | | |||     ||||| | ||| | || |  | |  ||||| ||||| ||||||||||||||| ||||||||||||||||||| || | |||||||||||||||||| | |
tgattgaatctgttaa--ggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG

upper sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G14260.2 (Arabidopsis thaliana), 3'ss of exon 2
gtctaaccgcctacctaagtttgtctt--ttaccat-----cctgtatgtgcaaaccattgcataaatctgtttgctaattttgttatactacatctgttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG
   ||      | | | | | | || |  | || ||     ||| ||  |    | ||  |   | || ||  |  | | |||    |  ||| |   |  |  ||||||||||||||| ||||||| ||||| ||||| ||||| || ||  | || || || |||||||| ||| ||
--gtagttttttccttcattgtttcatgatcactataggaacctatagttagttatcaa-gagaacatttgagtattgacttttaagttttacgt---tgtgatcagTATGCTCACAGAAAATGTGTTCAACGTTGGTGTAATGAAAAGGGAAACACTATATGCGAAATCTGTCATCAG

upper sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G62460.1 (Arabidopsis thaliana), 3'ss of exon 2
--gtctaaccgcctacctaagtttgtcttttaccatcctgtatgtgcaaaccattgcataaatctgtttgc-taattttgttatactacatctgttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG
  |   |       |   ||  |  |  |||    |  | |   ||  | |  | |  |||| | |||  | | | |||| |||  |   |||      | ||||||||||  |  | ||||| ||||| ||||| ||||||||||| || |||| ||||||||| |||||  ||
gtgataattttatcaatgaatctcattgttttatttgtttttgttggtatctttcgtttaaaacagttctcatcaatttggtattttgtgtct------atagTATGCTCATCGTAAGTGTGTTCAACGTTGGTGTAATGAGAAAGGCGACACAACCTGTGAAATATGCCACAAG

upper sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
gtctaaccgcctacctaagtttgtcttttac-catcctgtatgtgcaaaccattgcataaatctgtttgctaattttgttatactacatctgt-tcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG
    | || || ||  |      |     |    |    | |||     |  | | || | |   |   ||| |       |   || ||||| ||   |||| |||||| ||  ||||||| ||||||||||||||||||||||| |||  ||  || || ||||| ||| ||
--acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcctagactagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG

upper sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 4
gtctaaccgcctacctaagtttgtcttttaccatcctgtatgtgcaaaccattgcataaatctgtttgctaattttgttat--actacat-ctgttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG
     |  | |    | || |    |||     ||||  || |      |  |   |  || |||  |  || ||||||||  |||  ||  | ||    ||||||||||| ||  | ||||| ||||||||||||||||||||||| || | ||| ||||| ||||||||| ||
--tgtattgtcattatgagataaaatttagtactccttgatatttttctctctaactccat-tgtcagtcaaatttgttattgactgtatattttttttccagTATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAG

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|76909618|gb|DV163452.1|DV163452
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|31558678|gb|CD527890.1|CD527890
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|71332393|gb|DR803153.1|DR803153
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|29130457|gb|CB381161.1|CB381161
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|31406064|gb|CD484796.1|CD484796
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|28390336|gb|CB250165.1|CB250165
EST:     CTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: CTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|29130571|gb|CB381275.1|CB381275
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|28873794|gb|CB329735.1|CB329735
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|211448719|gb|FL094703.1|FL094703
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|211010477|gb|FL237651.1|FL237651
EST:     CCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGTCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: CCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTG-CAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|76013718|gb|DT940888.1|DT940888
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAGCGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGAGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|22818791|gb|BU498881.1|BU498881
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|101402591|gb|EB822839.1|EB822839
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|29947111|gb|CB816487.1|CB816487
EST:     CCTCAGGAAGAACCTCTTA-TTTNCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: CCTCAGGAAGAACCTC-GAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|211448717|gb|FL094701.1|FL094701
EST:     ACCTCAGGAAGAACCTCGARAGCCCCTGCGCTTGCAACGGCAGCCTCAAR                         TATGCTCACARAGAATGDGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|30307008|gb|CD001681.1|CD001681
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|211010485|gb|FL237659.1|FL237659
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|76936722|gb|DV174850.1|DV174850
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAG                         TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACA
EST: gi|74242887|gb|DT650801.1|DT650801
EST:     ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCCAG                         TATGCTCACAGAGAATGT
genomic: ACCTCAGGAAGAACCTCGAGAGCCCCTGCGCTTGCAACGGCAGCCTCAAGgtgcgtgctg ... gttcgcacagTATGCTCACAGAGAATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaccattgcataaatctgtttgctaattttgttatactacatctgttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG
                     tgctaat  putative branch site (score: 2)
                                          tctgttc  putative PPT
                        taattttgttatacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctaaccgcctacctaagtttgtcttttaccatcctgtatgtgcaaaccattgcataaatctgtttgctaattttgttatactacatctgttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG

- - - - - - - - - - - - - - - - - -ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - -cattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacatc