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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcatctttgctgcaggaagtcgtcgaacatagtcacaatgtttttttaaaaagcagaagtttctaaaccgctgattcctgaaagctgtcacttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG

Basic information

species Zea mays
transcript GRMZM5G841900_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841900_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g57070.1 (Oryza sativa), 3'ss of exon 2
ggcatctttgctgcaggaagtcgtcgaacatagtcacaatgtttttttaaaaagcagaagtttctaaaccgctgat--tcctgaaagctgtcactt---ttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG
      || |  |||        | |      ||   |  | || | | | |  |    |  | ||| | ||| ||  |  || | |   |  ||    |||||||| || |||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| |||  |||||||||||||||||||||||
---tggttagtggcactggtcaattgtctgctgtt-tagggattatctgagatacttttgcatgtaa-ctgctcataattttgcatgtgctggctgacattgcagGTGACGAAGGTTATGGCTAGGATGGCTTCTGCAGATATAATGTGTGTTGACTCAAAGGCTGTCAAGGAAAAGTTCACTGGCATGATAAG

upper sequence: GRMZM5G841900_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0043g00400.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------------------------------ggcat-ctttgctgcaggaagtcgtcgaacatagtcacaatg--tttttttaaaaagcagaagtttctaaaccgctgattcctgaaagctgtcacttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG
                                                                                           ||  |||  ||     | |    | |  |  | | ||    || || |||| || |     ||    |   |  |    |     ||| |  | |   |||| || || |||||||||||||||||||| || ||||| |||||||||| | | ||| || |  ||||||| || ||||| || || ||
gtaagtttcttcaatatttatctctgttcatttattttgatgatctcttgtatatacatgctgcaacttattcatcaatcagcagcattatatgtttttttgggttcaattcaaggatttcattataagaatttcttctaaacagaattgagtttgggatgaccaagatttatcctctggc-ttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGCCCCAAGTCTGTGCGAGAAAAATTTACTGGAATAATTAG
















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|211102908|gb|FK962289.1|FK962289
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118860|gb|FL110175.1|FL110175
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|32796285|gb|CD948521.1|CD948521
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102904|gb|FK962285.1|FK962285
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118861|gb|FL110176.1|FL110176
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118854|gb|FL110169.1|FL110169
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|76012394|gb|DT939564.1|DT939564
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118858|gb|FL110173.1|FL110173
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102910|gb|FK962291.1|FK962291
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118856|gb|FL110171.1|FL110171
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTYGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118859|gb|FL110174.1|FL110174
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102909|gb|FK962290.1|FK962290
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102911|gb|FK962292.1|FK962292
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|148939988|gb|EC884719.2|EC884719
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|74244670|gb|DT652584.1|DT652584
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|50328543|gb|CO523669.1|CO523669
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102902|gb|FK962283.1|FK962283
EST:     CAAGGCCCATGGAGCTGTGCCACAGCCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: CAAGGCCCATGGAGCTGTGCCGCAGCC-GGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|71428020|gb|DR809070.1|DR809070
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211102903|gb|FK962284.1|FK962284
EST:     ACAAGGCCCATGGAGCTGTGCCACAGCCGGGAAGCGTTGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGACATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118857|gb|FL110172.1|FL110172
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|6827420|gb|AW331063.1|AW331063
EST:     GCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: GCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaaaagcagaagtttctaaaccgctgattcctgaaagctgtcacttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG
                                           tcactttt  CT-rich tract
               tttctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcatctttgctgcaggaagtcgtcgaacatagtcacaatgtttttttaaaaagcagaagtttctaaaccgctgattcctgaaagctgtcacttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG

- - - - -gctgcag
- - - - - - - - - - - - -gaacata
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcagaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatt