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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcatatatgactgcaaccatgttaccattgccgtaataatatgattattgcacatctaaaatctcactttgcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA

Basic information

species Zea mays
transcript GRMZM2G109383_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 8
gtattcatatatgactgcaaccatgttaccattgccgtaataata--tgattattgcacatctaaaatctcactttgcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA
||| ||   | |  |   ||| ||| |  |  |  | | ||| ||  ||  | |||||||||| ||   |   |||||||||| ||||||||||| |||||||||||||| ||  |||| || | || |||||||||||||||||||||||||| |||||||||| ||||||| ||||| ||||| 
gtactcgcttttatcctgaactatgctcaccctctcctcatattaactgcctgttgcacatctgaacctttggtttgcacttttagTTATGATGCTCTCCATGGTGTTGCTGGGACTTACGCAACACGCATCTTTGTGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG

upper sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 9
--------------------gtattcatatatgactgcaaccatgttaccattgccgtaataatatgat------tattgcacatctaaaatctcact-----ttgcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA
                     |  |  | |||  |||     || ||    ||   | |||| | |  |      |  || | | || || | |   |     ||    ||  |||||||||||||| ||||| ||||  ||||||||||| || |  || ||||| ||||||||||||||  | ||||||||| || |||| || || || || 
gtatatagtaggcctcttagttggttctttattgctgagtatatatttttttttttggaatatttttttggaatctggtggataccttaacttttgttcaatgttatttttaaagTTATGATGCACTGCATGGAGTTGGTGGAGCTTATGCAAAGCGAATATTTGTTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG
















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|31349456|gb|CD433813.1|CD433813
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCGCTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|211126281|gb|FL366445.1|FL366445
EST:     GACTTCGAAGCAATAAAAA-GCTGCTGACCTCCCCAAAGTTTACATTCTG                         T-ATGATGCACTCCATGGTG
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTG
EST: gi|67035308|gb|CO463841.1|CO463841
EST:     ACTTCGAAAGCA-TAAAAA-GCTGCTGACCTCCC-AA-GTTTACATTCTG                         GTATGATGCACTCCATGGTGNTGCGGGAGCTTATGCCCAACACATCTTTGT
genomic: ACTTCGAA-GCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|67018536|gb|CO447285.1|CO447285
EST:     GACTTCGAAGCAATAAAAAA-CTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|60351626|gb|DN218599.1|DN218599
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|149013083|gb|EE042782.2|EE042782
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATG
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATG
EST: gi|67025909|gb|CO454658.1|CO454658
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|31353391|gb|CD437748.1|CD437748
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCGCTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|67022599|gb|CO451348.1|CO451348
EST:     GACTTCGAAGCAATAAAAAA-CTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|60351436|gb|DN218409.1|DN218409
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|31353888|gb|CD438245.1|CD438245
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCGCTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|149017022|gb|EE045668.2|EE045668
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACA
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACA
EST: gi|31356494|gb|CD440851.1|CD440851
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCGCTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTT
EST: gi|67041650|gb|CO467905.1|CO467905
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|84980113|gb|DW530462.1|DW530462
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCGCTCCATGGTGTTGCGGGAGCTTATGCCAAACACAT
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACAT
EST: gi|148945380|gb|EC890603.2|EC890603
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATGGTGGTGCGGGAGCTTATGCCAA
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAA
EST: gi|211101215|gb|FL335616.1|FL335616
EST:     ACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAAGTT-ACATTCTG                         TTATGATGCACTCCATGGNTGT-GCGGGGAGCTTATGCCAAACACA
genomic: ACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAA-GTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGG-TGTTGCGGG-AGCTTATGCCAAACACA
EST: gi|149099504|gb|EE185542.2|EE185542
EST:     ACTTCGAAGCAATAAAAA-GCTGCTGACCCTCCCCAA-GTTTACATTCTG                         GTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
genomic: ACTTCGAAGCAATAAAAAAGCTGCTGACC-TCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGT
EST: gi|149014023|gb|EE043541.2|EE043541
EST:     GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTG                         TTATGATGCACTCCATGGTGTTGCGGG
genomic: GACTTCGAAGCAATAAAAAAGCTGCTGACCTCCCCAAAGTTTACATTCTGgtattcatat ... gcactttcagTTATGATGCACTCCATGGTGTTGCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgccgtaataatatgattattgcacatctaaaatctcactttgcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA
                                   atctcac  putative branch site (score: 3)
                                              cactttc  putative PPT
        taataatatgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcatatatgactgcaaccatgttaccattgccgtaataatatgattattgcacatctaaaatctcactttgcactttcagTTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA