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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

Basic information

species Zea mays
transcript GRMZM2G042074_T01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggaca-ccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                         ||  | |  ||||   |  ||  |||||   ||     || | ||| || | |  |||  | ||||   | | || | || |  ||||||     || | ||||||||||||||| |||| ||||| || |||||||||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||
----------------------------------------gtaagtaaattgtaattgatcaatcacaacgcct-----ttctgaattccctgt-gatgtttgctttctagtttatct-tcttcatcttgt----gttgtatagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                         | |||| |    | |  || | || | |   | |  | |  | |||  | | ||| | | |  |  ||||         | | || | |||| |  ||    |       | |   |||||||| | ||||| || || || || |||||| | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
-----------------------tgaagaactaaacatttaaatctcatattttttatggtagc-tactat--ggattttcttagtttca-atta---------tctgtgttgatttgttgtggcaat-------tgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatc-ctgctcttgtttttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                        | | |      |||  |||  || ||   |  |   | ||    |          ||| | |   ||  | | | || |  | | ||||||||| ||||| |||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | ||||
------------------------------------------------------gtaagccttttgtataaatgttcttagtttgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttct--tgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgc-tcatttatcctgctcttgttt---ttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                          |  | |    |      |  || | |||   |||| ||| |||    | |    | | | |       ||||| |   || || | ||||||||| ||||| |||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || |||||||||||||||||  |  | ||||
----------------------------------------------------------gtaagccttttgcacaaatgtttttaattt-gtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 19
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgta-gtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttatt-ttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                         ||| |  | | ||        || ||  |   | |    |||||     |    ||  |    || ||| |||||||  ||||| ||||  |  |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
-------------------------------------------------------------------------gtaagccttttaacttaagggtattgttt-tgtattgattcattggatgtaactttactagctttgtttcagGTTGACAGCATGTTGGGTCGTAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACGA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 22
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaat--cccgtattaatgcatacttttctgctcatttatcctgctct--tgtttttattttt-tagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                |    |||   |||    ||| ||     |||    ||  |   ||| |||        ||    | || | |  || | |  |||    ||| |   |||||||| | ||||| || || || || |||||| | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
------------------------------------------------tgaagacctaaacatttaaatctccaattttttatgatagctactatgaattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTAGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttatt-ttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                         |||     |  | ||     || ||  |   | |    ||||| |   |    ||  |    || ||| |||||||  ||||| ||||  || |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
-------------------------------------------------------------------------gtaagccttttaaccaagggtattgtgt-tgtattgattcattgaatataactttactagctttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccac-aatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttt-tagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                          ||  | | |||  |  |||   |  || | || |  |    |  |    ||  | | | |  || | |    || | |  ||  |  | |   | || | ||||||||| ||||||||||||| || ||||| || |||||||||||||| |||||||||||||| || || || ||| | |||||||| ||  |  | ||||
------------------------------------------atgaggtatgttgctagacgttaagaacagctctcat--acctgtttattac-agttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccac-aatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttt-tagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                | |||  |  |||   |  || | || |  |    |  |    ||  | | | |  || | |    || | |  ||  |  | |   | || | ||||||||| ||||||||||||| || ||||| || |||||||||||||| |||||||||||||| || || || ||| | |||||||| ||  |  | ||||
-----------------------------------------------gtatgttgctagacgttaagaacagctctcat--acctgtttattac-agttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 22
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctc-atttatcctgctcttgtttttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                   | | |||    ||| |  |  ||    |     | |||      | | || || || ||  |   ||||||   | ||   | ||  ||         | ||| || |||||||| ||||| |||| || || || || || || ||||||||||| |||||||||||||| || ||||| ||||| |||||||||||| | |||||||
----------------------------------gtatgtttgaa-gatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtgg----aaaatcattattcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATGCGTAAGATGAAGAACGAGTTCATGGTAAACTGGGATGGTTTAAGAACAA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
-----------------------------gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccag-gacaccacaatatctgtagtttgtcaatcccgtattaa------tgcatacttttctgctca----tttatcctgctcttgtttttatt-ttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                               || || |  || |  |||    ||       | |   |  ||    |  ||  | |  ||    ||||   | || || | || ||   | || |      | | |  ||| ||| | |    |||||  |   |||   |||||| ||| |||||||  ||||| | || || || || || || |||||||||||||| ||| | || ||||| |||||||| ||||||||||||||||| ||  | ||||
gtaagttgaataaatctttaaattcatccacaacttttgcta-taatgttcctcactctttttatgggtccatggatttagtgacggtaactgttcaatccttttaattcgccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaacttagatttattgtttcagGTTGACAGCATGTTAGGGAGACGTGAAAATCCAGGAGAACATGAAGCTATGAGGAAAATGAAGAATGAGTTCATGGTGAACTGGGATGGCCTACGTACAA

upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 23
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                         |  |  || |  |    |  |||||  ||    ||||  |   | | | ||||||   |     |  ||||  |||  | ||  |||||||| ||||||||||  || ||||||| || || |||||||| |||||||||||||||||||| || |||||||| |||||||||||  || | ||||
-------------------------------------------------------gtgagcttcatataactctt--tttgtttat---atattgtttgcttcctctctgcttgcta----tattctttgtttggtctt--agGTTGATAGCATGCTGGGCCGGAGGGAGAATCCAGGGGAACATGAGGCCATGCGTAAGATGAAAAACGAATTTATGGTCAACTGGGATGGCTTGCGCACAA

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|67017525|gb|CO446274.1|CO446274
EST:     TTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAA                         GTTGATGGCATGCTGGGAAGGCNGGAGAACCCTGNAGA-CATGAAGCCATG
genomic: TTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttata ... tattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATG




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 126

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttata ... tattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 228

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttata ... tattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 142

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttata ... tattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 284

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttata ... tattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
  tattaat  putative branch site (score: 284)
                          tttatcctgctcttgt  putative PPT
                                    tcttgtttttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG