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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

Basic information

species Zea mays
transcript GRMZM2G409190_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgccct-tgtt-tttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                                   ||  |  | ||||   |  ||  | || | |    |  | || | ||| |  | | ||||  | |||||  | | || |       | | |||| | |||||||||||||||||||| ||||| || ||||| |||||||||||||| ||||| || ||||||||||||||||||||||||||||||||||| |||||||
--------------------------------------------------------------------------------------------------gtaagtaaattgtaattgatca--atcacaac----gcct-ttctgaattccctgt-gatgtttgctttctagtttatcttcttcatcttgtgttgtatagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagt--ttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                                 |  |   |||    |     |   ||   | | | | ||   |  | |  ||  | | | | | ||    |   || | |||| |  || |  |  |   |||||||| | ||| | || || || || |||||  | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
-------------------------------------------------------------------------------------------------tgaagaactaa-acatttaaatctcatattttttatggtagctactatggattttct-tagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctata-ttgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                                   ||   ||  ||||  |          || |   ||||||||  ||||| | | |  |||   |||  |   ||   | |  |  || | |  | | ||||||||| |||||||||| ||| |||| || || || || ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | ||||
--------------------------------------------------------------------------------------------------gtaagccttttgtataa----------atgttcttagtttgt-atcaattcaacagctgaaaaataaatcagtgaaaactagta-tggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                                   ||   ||  || || |          || | | || |||||    | || | |  ||    |||  |   |    | || |  || | |  | | ||||||||| |||||||||| ||| |||| || || || || ||||| |||||||| |||||||||||||| || |||||||||||||||||  |  | ||||
--------------------------------------------------------------------------------------------------gtaagccttttgcacaa----------atgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgta-tggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 19
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                                                    |  | |    || ||  ||  | ||||      | ||||||| |||   |   ||    ||||  ||  | ||||||  |||||||  ||||||||||  |  |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
--------------------------------------------------------------------------------------------------------------------gtaagccttttaacttaagggtattgtt----ttgtattgattcat---tggatgtaacttta--ctagctttgtttc-agGTTGACAGCATGTTGGGTCGTAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACGA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 22
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                               ||   |  |  ||  |   |     | |   | | ||     |  | | |||  | | | | | ||    |   || | |||| |  || |  |  |   |||||||| | ||| | || || || || |||||  | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
-----------------------------------------------------------------------------------------------tgaagacctaaac-atttaaatctccaattttttatgatagctactatgaattttct-tagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTAGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcct---gctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                                                                  |     || |   |||   |||  || || ||   ||| |       |  | | ||  | ||||||  |||||||  ||||||||||  || |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
---------------------------------------------------------------------------------------------------------------------------------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttc-agGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccac-catatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                            |   || | || |||       || ||| | | |||| ||||   ||   ||   |  | | ||  || |||  ||           |||       ||    ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| ||  |  | ||||
-------------------------------------------------------------------------------------------atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttt-tctttctgaatatcttttgaacgg--gatcaaaattatg----tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccac-catatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                                || | || |||       || ||| | | |||| ||||   ||   ||   |  | | ||  || |||  ||           |||       ||    ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| ||  |  | ||||
------------------------------------------------------------------------------------------------gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttt-tctttctgaatatcttttgaacgg--gatcaaaattatg----tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 22
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                  ||   |||  |  ||| |  | | || ||||||   | | ||  |     ||  |||   | | | | ||   || || |||  ||  |  || | | |        ||||               || |||||||| |||||||||| || || || || || || ||||||||||| ||||| |||||||| || ||||| ||||| |||||||||||| | |||||||
-----------------------------------------------------------------gtatgtttgaagatattaaaaagcgttctctgttctctcccacctt----tgaagccagtctttttat-gtactttctcgatctgatgattgtggaaaat--------catta--------------ttcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATGCGTAAGATGAAGAACGAGTTCATGGTAAACTGGGATGGTTTAAGAACAA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
||| ||     |  |  |  |  | ||| |        |||||||  | ||     |      |||| |     |   |||| |   ||  |  ||||| | | ||  |    |   |  |      |||| |||||| ||     || | |  || |  | | |||  || | | |||   |    ||||||  |||||||  ||||||| || || || || || || |||||||||||||| ||| |||| ||||| |||||||| ||||||||||||||||| ||  | ||||
gtaagt-tgaataaatctttaaattcat-ccacaacttttgctataat-gttcctcactctttttatgggtccatg--gatttagtgacggtaactgttcaatccttttaattcgccattctg----atctttagtttctttct--tcttttcctgttaaaaaatttattgttaacttagatt--tattgtttc-agGTTGACAGCATGTTAGGGAGACGTGAAAATCCAGGAGAACATGAAGCTATGAGGAAAATGAAGAATGAGTTCATGGTGAACTGGGATGGCCTACGTACAA

upper sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 23
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatt-tatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                                                    |  | |  |||||        | || |   |  ||||||| |   | | |  |||||   | ||| ||    ||| | |||||||||| ||||| ||||  || ||||||| || || |||||||| |||||||| ||||||||||| || |||||||| |||||||||||  || | ||||
--------------------------------------------------------------------------------------------------------------------gtgagcttcatat-----aactctttttgtttatatattgtttgcttcctctctgcttgctatattctttgtttggtcttagGTTGATAGCATGCTGGGCCGGAGGGAGAATCCAGGGGAACATGAGGCCATGCGTAAGATGAAAAACGAATTTATGGTCAACTGGGATGGCTTGCGCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
         tattgat  putative branch site (score: 3)
                                     tcctgcccttgttttt  putative PPT
       tatattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG