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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG

Basic information

species Zea mays
transcript GRMZM2G300412_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 7
gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
|||  | ||||| | | | |  |  | |  ||||    |   ||||| |||  ||  |   |||||| |||||   || | || | ||  ||   |||||| || |||||||| ||||| |||||||||||||| || || ||  |||||||||||||||||| ||||||||||||||
gtacgtctgttc-tatcacaaatacactacatttatcctatattttcttaatctag-tgcaaagttcacttac---ttgaattgatttacttc--atcagGAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaacttt----ttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
  ||   |  ||  ||  ||| |  |  |||| ||   |  ||| |||| |  | |   |    | || |||    |    | ||| |     | |     |||| ||| ||||||||||||||||||| |||||||| || || || ||||||||||| ||||| | |||||| || || |
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 7
-gtaaatttgttcatctgaaatttgaaatttattt--gctttggtttttcataa-attatctttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
  | |  |  || ||   |  || ||  ||| |||  ||   |  ||||  ||| |  || | | | | |||   | |   ||  |||  | | | | || |||| ||| | ||||| ||||||||||| || ||||| ||||| || ||||||||||| ||||| | ||||||||| || |
tattagctccttaatgcaaggtt-gacttttttttaagcaaagaatttttttaatacaatgtattatggtct---aaacacttgattatatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
-gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttat--ttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
    ||||||      |||   | ||  || || |        |  | ||   ||    |     ||     | ||  | |   | ||  | | |   | |||| ||| ||||||||||||||||||| |||||||| || || || ||||||||||| ||||| | ||||||||| || |
taggaatttg---gaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
------gtaaatttg-ttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
      | ||  ||   |  | ||||      ||||| ||   |    | |||    |  | | ||     |  ||| |    || |||    | | | | || |||| ||| | ||||| ||||||||||| || ||||| ||||| || ||||||||||| ||||| | ||||||||| || |
cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtatt----atggtctaagcacttgatta---tatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 8
gtaaatttgttcatctga-----aatttg---aaatttatttgctttgg--tttttcataaattatctttcaagttctcttacagtttta---------tttaacttttt--ttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
||| |||  ||||| | |     || |||   ||     | |  |  ||   | ||  |  ||  | ||  |  |  |  || || | ||          |||| | | |  |  ||||||| ||| | ||||| ||||||||||| || || || |||||||| ||||||||||| || || | ||||||||| ||||
gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttatacatattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttat---ttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
               |   | |  | | ||||  |||||   || ||  || ||||||  |  ||    | ||| | ||||   ||   || | || |   |||||||||||| ||||||||||| || |||||||| |||||||| |||||||||||||| |||| ||| ||||| ||||
--------------gtaggagtaaacacttatcagcttttaattctc--aacttatctg-cgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
-gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatc----tttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
  ||   ||  || |||     ||  ||   |||         | || | |||||||     |||      |||    |   |  | | ||||   ||    |||||||  |||| || ||||||||||| |||||||| |||||||| ||||||||||| ||||| | ||| ||||| || |
aatactgttactcttctttctcttttaaa--attgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgactta---cagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 7
gtaaatttgttcatctgaaattt---gaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaactttttttctat------cagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
       |      |||| ||||   |    |   ||  |||  | |   | |||  | ||||    |     ||   || ||| |  |||   || |||      |||| || |||||||| ||||||||||| ||||| || ||||| ||  |||||||||| ||||||| ||||||||| || |
-------tagcagactgacatttttggcggctctgttaattttatgtaggaaaaaagacctttt--ctctaactatgattctatatgccttccgttatatatattacagGAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: EFJ17446 (Selaginella moellendorffii), 3'ss of exon 6
gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
                                       |    | ||  |  ||| | ||  ||   ||  | | |        | || |  | | ||||||||||||| || || || ||||| || || || || || |||||||||||||||||||||| |||||| || ||||
---------------------------------------gtacgtgcaccagatatttgtcttgtctactgcctgct--------cattgtgccgagcagGTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
lower sequence: EFJ35029 (Selaginella moellendorffii), 3'ss of exon 6
gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
                                       |    | ||  |  ||| | ||  ||   ||  | | |        | || | || | ||||||||||||| || || || ||||| || || || || || |||||||||||||||||||||| |||||| || ||||
---------------------------------------gtacgtgcaccagatatttgtcttgtctactgcctgct--------cattgtgtcaagcagGTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcataaattatctttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
                                  atttaac  putative branch site (score: 3)
                                   tttaactttttttct  CT-rich tract
                        ttacagttttatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA