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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

Basic information

species Zea mays
transcript GRMZM2G021514_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 4
---------gtatgcttaacccat-ctcatcagactgcgcataaccaaatatgcat-atgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
          |||  || |    |  |||||      |   ||  |   |    ||  |    ||   |||    || ||  ||  ||  | ||  | |||||||||||||| || || ||||| |||||||||||  | ||||| || || |||||||| ||||| || ||||||||||| |||||||| |||||||| ||
cttattctgttatcatttatttttattcatctcttgtcttgtattcttgttcatattgtacttcccaagttcattttttactgcattctttctg--cctcagATGAAAAGATAGCCTTGCTGGGTGCCATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTATGGACTCCTGCATTGAGCCCAAATGATGA

upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 4
---------gt-atgcttaacccatctcatcagactgcgcataaccaaatatgcat-atgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
         || ||  || |      |||||      |   ||  |   |    ||  |    ||   |||     | ||   |  ||  ||||  ||||||||||||| || || || ||||| || ||||||||  | ||||| || || |||||||| ||||| || || |||||||| |||||||| |||||||| ||
tcttattctgtgatcttttattttattcatctcttgtcttgtattcttgttcatattgtacttcccaagttcattgtttactacattc--tttgtgcttcagATGAAAAAATAGCCTTGCTGGGTGCTATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTGTGGACTCCTGCATTGAGCCCAAATGATGA

upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcttaacccatctcatcagactgcg-cataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatct--tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
||     |    | |  | |  |  |  | ||||    ||||||  | ||   || |  ||   |||| |       || ||| ||    |||||||| ||||| |||||||| || || || |||||  ||||||| || ||||||||||| ||||| || || |||||||| || ||||| ||||| |||||
gtgaatctcttaccttaccttggtttttgacatactgtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA

upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgcct-----tctaacgctgtccat--ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                                      |  | || ||   |     ||    | |     | |    ||  || || || || ||||| |       |||||| |  || ||  ||  |  |||||||||||||||||||| ||||| || || |||||  | || || | ||| |||||||| ||||| ||||| ||||| |||||  | || ||||| || ||
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttctcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA

upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
--gtatgcttaacccatctcatcagactg----cgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtc-catttgatct---tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
   |||  |    |  |||  |  || |        ||      |  |   | |   |  | | |||   || |||   |||    ||| || |   |||||||| || || ||||| ||||| || ||||||||  | ||||| || || |||||||||||||| ||||| |||||||| || |||||||| ||||||||
atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattt-tctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA

upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 4
----gtatgcttaacccat---ctcatcagactgcg-cataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatt-tgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
    || ||||   || ||    | |||   |||   | | | |   |  |  | |    ||| | || |   | ||    | |   |  ||   ||||||||| || ||||| || ||||| || || ||||| |||||||| ||||| ||||| || ||||| ||||| |||||||| ||  | || |||||||||||
cattgtttgctatcccaatgggtttatccatctgtttcctcatcttttcagttttttcctcctttcttggagctttagtattatgtttcatgtggttcagATGAGAAAATTGCGTTGCTGGGTGCAATTCAGTCGTTGTTTGAAGGCTCAATGTATACTTTTGTGTTCCTCTGGACTCCTGCTCTAAGCCCAAATGAAGA

upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgt-ttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                                                                                      || ||||       |    | |||  | | ||     |  |  || |  ||  |    |  ||  || | |   |||| | |  ||   ||||||| ||||| ||  |  |||| ||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||  |
gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtac--tgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtc-actgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA

upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------------gtatgcttaa----cccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccat-ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                                                                                |||||| |     | || ||  | |   ||   |   ||   ||    ||       |  || |  |  ||    |||  || ||| | | ||||||||||||||||  |  |||| || || || || ||||| || || |||||||| |||||||| ||||| ||||| ||||||||||||||  ||||  |
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttact--tgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA

upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ21113 (Selaginella moellendorffii), 3'ss of exon 4
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                     |  ||   |||  |   ||        ||  | | | ||||  |||||                 |  |||||||||||||||  | || ||||| || || ||  | || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || ||  |
-------------------gtaagcttttcatgtctttatgcaagcgagagccttatctttggattcta-----------------tgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA

upper sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                            | | | |     |||  | | |  |  | |   ||||| |    || |  |||  || |  |||||||||||||||  | || ||||| || || ||  | || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || ||  |
----------------------------gta-agcttttcatgtctttaatgcaagcgagagccttat----ctttggattctatgt--agATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA
                                       tccattt  CT-rich tract
        atatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA