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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcag

Basic information

species Zea mays
transcript GRMZM2G113995_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113995_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g47110.3 (Oryza sativa), 5'ss of exon 3
----------------------------------------ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcag
                                        ||||| ||||||||||| |||||| | |||||||| |||||||| ||||| || |||||||| |   ||  |  |   | ||   | || ||     |  | |  || || |   | | |||  |   |    | ||||||||
CTTATTCCTATATGTTATTTTTGCACGTTCTGATTTGCAGATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAGgtttaataa--gctattttaagttatgctcatcagatagcttgccttgtt-agtgaagctaaggtttggtggctttgttgcag

upper sequence: GRMZM2G113995_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 4
ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcag
||||| ||||||||||| |||||| | |||||||| |||||||| ||||| || |||||||| |   ||  |  |   | ||   | || ||     |  | |  || || |   | | |||  |   |    | ||||||||
ATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAGgtttaataa--gctattttaagttatgctcatcagatagcttgccttgtt-agtgaagctaaggtttggtggctttgttgcag

upper sequence: GRMZM2G113995_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 4
ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctg----------taaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcag
||||| || |||||||| |||||||| ||||| ||||||||||| || || || ||||||||  |          |||    |    ||||    |  |||||| |  ||| ||||   |||   || ||| |         |  | || |||
ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtcctagataatgcatttatgtcaaacgtcttaattggttgattagtttc--tcagttagtttacttatt-----tcttctttcag

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|211484925|gb|FL394381.1|FL394381
EST:     TTGATTCGTTGGATCGGGAGAGA-TTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|33771194|gb|CF273373.1|CF273373
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|211029880|gb|FL404674.1|FL404674
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|211290604|gb|FL410977.1|FL410977
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTG
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTG
EST: gi|211461841|gb|FL417627.1|FL417627
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGA
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGA
EST: gi|211212184|gb|FL397467.1|FL397467
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|33103749|gb|CF063709.1|CF063709
EST:     TTGATTCGTTGGATCGAGAGAGAATTGGAAAAGCCAAATCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGT
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGT
EST: gi|211266589|gb|FL404010.1|FL404010
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|211141968|gb|FL418185.1|FL418185
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAAGTGTAATACTGGTACTTGC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACA-GTGTAATACTGGTACTTGC
EST: gi|211156685|gb|FL406071.1|FL406071
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|9731677|gb|BE510429.1|BE510429
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|211334235|gb|FL381816.1|FL381816
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|211115280|gb|FL397760.1|FL397760
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAAT
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAAT
EST: gi|211363304|gb|FL391107.1|FL391107
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGGANKCTTAACAGTGTAATACTGGTACTTGC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTG-ATGCTTAACAGTGTAATACTGGTACTTGC
EST: gi|211108318|gb|FL385993.1|FL385993
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|211466099|gb|FL374831.1|FL374831
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATTCAAAGATCCT
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAAT-CAAAGATCCT
EST: gi|9731678|gb|BE510430.1|BE510430
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|211060681|gb|FL415617.1|FL415617
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|5055809|gb|AI734696.1|AI734696
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAA
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAA
EST: gi|211198832|gb|FL369949.1|FL369949
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGGC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTG-C

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcag

- - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - -  AGCTGA