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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

Basic information

species Zea mays
transcript GRMZM2G095348_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatca-tgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
|||| |||| |||||| | ||  |   |  | |||   ||  |  || | ||     ||||   |    |   ||| ||| || |||| |||||| |||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| || |||||||| 
gtgagtcaaatattatctattgatatttatagattg-atacttttaacgaattt-catactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
--------gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
         |  || | ||   ||||  |  |  |      | || |   |   ||  ||  ||||| ||| |   | || || ||| ||  |    ||||| | ||||||||||| |||||||| |||||  |||| || || ||||||||||||||||| || |||||||||
gtaagtactttgattaggtgacatttagttatctgc-----tcttttccttcttattcatt-gtttaatataattttgttattaatcttgtgt---cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtgaatcaagtattattttttcttgg-gtggaaattttgtatgtaaaatgtatga--gtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
       ||||  |    |    ||   |     || ||  | ||     | | |  ||||  | ||||  || |    ||  |    |   ||||| | |||||||||||||||||||| |||||  | || || ||||||||||||||||| ||||| |||||||||
-----gtaagtgcttgcatgaggtgacatcagctttctgcttttatttcttcttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttat-agAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
       ||||  | |   |     ||    |  ||| |   |  | |   |     |  |  | |  |||  |  ||  | | | | | ||||| | |||||||||||||| |||||  ||||  | || || ||||||||||||||||| ||||| |||||||||
-----gtaagtgct-tgcatgaggtggcatcagctttctgcttttatttcttcttactgtttcttatttttgttaaatttttcttgtgtcagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcattta----tagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
       ||||| | |  ||   ||      | || | |          |     ||   | || |  ||   ||| | ||  || |      ||||| | ||||||||||| |||||||| |||||  |||| || |||||||||||||||||||| || |||||||||
-----gtaagtactttgattaggtgacatctagttatctgctcttttccttcttattcgttgtttaatttaattttgttatttatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
------------------------------------------------------------------------------------------gtgaatcaagtattatttttt----cttgggtggaaattttgtatg-taaaatgtatgagtttactattaaccttttc-tttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
                                                                                           |  |  |    |  || | |     ||    | |||    |  || ||           || ||| ||||| ||||  |||||      |||  ||||  |||| ||||| || |||||||| ||||||||||| || ||||||||||||||||||||||| |||| ||||
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgttt-cagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------------------gtgaatcaagtatt----attttttc-ttgggtggaaattttgtatgtaaaatgt----atgagt-ttactattaaccttttcttt--atcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
                                      |  ||||  | ||    ||| | || ||   |   | |||    || ||  |||    || ||| |   || ||||  |||  |   || |   ||||  ||||  |||| |||||||| ||||||||  |||| || || || |||||||| |||||||||||| | |||||||||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
gtgaat-caagtattattttttcttgg-----gtggaaat-tttgtatgtaaaa-tgtatgagtttacta---------ttaaccttttctttatcatgcatt--tatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
|| |   | |  || ||    | ||||     |||| | | |||  |||  | | || | || || | ||         ||   ||||||||| |  | || |  |  ||||| | || |||||||||||||| ||  | || || || || |||||||||||||| |||||||| |||||||||
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
--gtgaatcaagtattattttttcttgggtgg-aaattttg--tatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
   ||     |  |   ||  |||     |   |  |||||   |   | ||  ||  |||| | |      ||||   |  |       ||  ||||  |||| |||||||||||||||||  |||| ||||| ||||||||| ||||||| |||||| | |||||||||
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatt-----tctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
                        tattaac  putative branch site (score: 1)
                   tttactattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG