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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacagtaacgttttaagtcaaagcaacataatttggaacagagggggtatgatacagtaacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG

Basic information

species Zea mays
transcript GRMZM2G174204_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 4
---tacagtaacgttttaagtcaaagcaaca-taatttggaacagagggggtatgatacag----taacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG
      | | |  ||||  ||      ||   ||  ||   | |     | | |||||||      ||| ||| |  |  ||||||| | || |   ||||| | ||||| |||||||||||||| ||||||||||||| ||||||||||||||||||||| |||||  ||||||||
gtaagtactcatattttgggttgctaaaatgctatctttctataatctagatgtgatacacaagtcaacttttcactgttttgatcattcatatgctgtgaaacatagGTTCTCAGCAACACAATTAAGCAAAAGAGGATGGAAAAGGCTGGCAAATGGGAGGTTCCTTTGCCAAAG

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 4
tacagtaacgttttaagtcaaagcaacataatttggaacagagggg---gtatgatacagtaacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG
                     |    |||   ||| || |  |  |   || || |   | |   || || |  ||   | |  | |||||  |      ||||| || ||||||||||| ||||||||||||||||| ||||| || |||||||||||||| || || |||
-------------------gcatgttcatgtcttgaaagatggttgtgtgtgtgtttttgcagacttgtaagtaatc--tgatggctttctact----tttagGTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 4
tacagtaacgttttaagtcaaagcaacataatttggaacagagggg-gtatgatacagtaacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG
                     |    |||   ||| || |  |  | || ||     | |   || || |  ||   | |  | |||||  |      ||||| || |||||||| || ||||||||||||||||| ||||| || |||||||||||||| || || |||
-------------------gcatgttcatgtcttgaaagatggttgtgtgtgtgtttgcagacttgtaagtaatc--tgatggttttctatt----tttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAG

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 4
-tacagtaacgttttaagtcaaagcaacataatttggaacagagggggtatgatacagtaacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG
  |   | | || || |   || |        |||             |    |   ||||   || |  ||| |  | ||  ||||||  |      ||||| || |||||||| || ||||||||||||||||| ||||| || |||||||||||||| || || |||
gcatgttcatgtcttgaaagaaggttttgccttttttt----------ttcagtcttgtaag--ttgaaagcaatc-tgacaaatttctatt----tttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
-tacagtaacgttttaagtcaaagcaacataatttggaacagagggggtatgatacagtaacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG
 |    |    ||||   |  |||       || |  ||         | | |    || |||    ||  |||| |  | || | | |  |   | |||||| || |||||||| || || ||||||||||| || || |||||||||||||| || || || ||||||
gtttgtttgttttttcttttcaagttgagatatctataattc------tgtaacttggtgacgg--cattacattaacaagtg-tgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG

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|8366902|gb|BE049910.1|BE049910
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|78109120|gb|DV527537.1|DV527537
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|37398604|gb|CF636617.1|CF636617
EST:     GTGCTCTTCCTCGGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|71440545|gb|DR821595.1|DR821595
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211464729|gb|FL207495.1|FL207495
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211464737|gb|FL207503.1|FL207503
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGAYACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAA
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAA
EST: gi|166510769|gb|EG093482.1|EG093482
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAG
EST: gi|14883663|gb|BI273476.1|BI273476
EST:     GTGCTCTTCCTCCTTATCTACTCGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAA
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAA
EST: gi|149079698|gb|EE168699.2|EE168699
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211296298|gb|FL480002.1|FL480002
EST:     CGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: CGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|15053622|gb|BI359167.1|BI359167
EST:     GTGCTCTTCCTCCTTATCTACTCGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211464732|gb|FL207498.1|FL207498
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAA
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAA
EST: gi|71440546|gb|DR821596.1|DR821596
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|148933462|gb|EC877158.2|EC877158
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|15053623|gb|BI359168.1|BI359168
EST:     GTGCTCTTCCTCCTTATCTACTCGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|60350420|gb|DN217393.1|DN217393
EST:     GATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211487760|gb|FL392997.1|FL392997
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|60340980|gb|DN207953.1|DN207953
EST:     TCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: TCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|50332541|gb|CO527667.1|CO527667
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|22545768|gb|BU098142.1|BU098142
EST:     GTGCTCTTCCTCCGTATCTACTCGATCGTGATCAGACACAGCGTGCCAAG                         GTCCTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|31359359|gb|CD443716.1|CD443716
EST:     GTGCTCTTCCTCCGGATCTACTGGATCGGGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211464730|gb|FL207496.1|FL207496
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|15313826|gb|BI478973.1|BI478973
EST:     GTGCTCTTCCTCCTTATCTACTCGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211462214|gb|FL207491.1|FL207491
EST:     GTGCTCTTCCTCCGTATCTACTCGATCGTGATCAGACACAGCGTGCCAAG                         GTCCTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTG
EST: gi|76917038|gb|DV166648.1|DV166648
EST:     GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAG                         GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|22819549|gb|BU499639.1|BU499639
EST:     GTGCTCTTCCTCCGTATCTACTCGATCGTGATCAGACACAGCGTGCCAAG                         GTCCTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAGCGTGCTAAGgtggattact ... tgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatgatacagtaacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG
                 ttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagtaacgttttaagtcaaagcaacataatttggaacagagggggtatgatacagtaacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - -caacata
- - - - - - - - - - - - - - - - - -gaacaga