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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttccttgagataacattttaaattccagagttttgttgggtttatgattatgaccagttatacatggtaactctttatgcacgtttcgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG

Basic information

species Zea mays
transcript GRMZM2G113995_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113995_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 3
tttcttccttgagataacattttaaat-tccagagttttgttgggtttatgattatgaccagttatacatggtaactctttatgcacgtttcgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG
|       ||  |||    |  | |   | |  |  |   ||   |  ||  | ||  | | |||| | |      | ||| ||||||||  || ||| ||||||| ||||||||||| |||||| | |||||||| |||||||| ||||| || ||||||
tactgaaattcggatgtattcatgagcatacccaactacattta-taaattgtaatagcaacttattcctatatgttatttttgcacgttctgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAG

upper sequence: GRMZM2G113995_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
---tttcttccttgagataacattttaaattccagagttttgttgggtttatgattatgaccagttatacatggtaactctttatgcacgtttcgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG
    | ||| |||   |  |  || |  |||      || | || ||||| || | |  |  |      ||   ||  | || |     || |  |  || ||||||| || |||||||| |||||||| ||||| ||||||||||| || || || ||||||
aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttg-taacaatgaagccctcaaccta--tgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
















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:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCCTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGA-TTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211423855|gb|FL404537.1|FL404537
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTCGAATCGTTGGATCGGGAGAGAA
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAA
EST: gi|33771194|gb|CF273373.1|CF273373
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211029880|gb|FL404674.1|FL404674
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCCTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211290604|gb|FL410977.1|FL410977
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211461841|gb|FL417627.1|FL417627
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCCTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211212184|gb|FL397467.1|FL397467
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCCTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|33103749|gb|CF063709.1|CF063709
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGAGAGAGAATTGGAAAAGCCAAATCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211266589|gb|FL404010.1|FL404010
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCCTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211141968|gb|FL418185.1|FL418185
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCCTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211156685|gb|FL406071.1|FL406071
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|9731677|gb|BE510429.1|BE510429
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211334235|gb|FL381816.1|FL381816
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211003691|gb|FL416464.1|FL416464
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCCTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211115280|gb|FL397760.1|FL397760
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211363304|gb|FL391107.1|FL391107
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCCTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211108318|gb|FL385993.1|FL385993
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211466099|gb|FL374831.1|FL374831
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|9731678|gb|BE510430.1|BE510430
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211060681|gb|FL415617.1|FL415617
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCCTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|5055809|gb|AI734696.1|AI734696
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCACCAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211198832|gb|FL369949.1|FL369949
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCT
EST: gi|211421603|gb|FL420626.1|FL420626
EST:     AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTG                         ATCTACGTAGTTGA
genomic: AAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAACAATACTGATGGCTTGgtatgtttta ... cgagttgtagATCTACGTAGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgattatgaccagttatacatggtaactctttatgcacgtttcgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG
                       tggtaac  putative branch site (score: 2)
                ttatacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttccttgagataacattttaaattccagagttttgttgggtttatgattatgaccagttatacatggtaactctttatgcacgtttcgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG

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