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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttttgtataaatgttcttagtttgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA

Basic information

species Glycine max
transcript GLYMA06G17940.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 23
gtaagccttt-tgtataaatgttcttagtttgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
||| || |     | |   |    ||  ||   || | |     |  ||   |    || |   | |   | |    | | | | |  ||||||||| ||| | || ||||| || ||||| ||||||||||| || ||||| ||||||||||| ||||| ||||||||||||||||| |||||||| |
gtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatgatccatacaaaatgcaacatttggca--gGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAAAACGAATTTATGGTGAATTGGGATGGATTACGCACTA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
gtaagccttttgta--taaatgttctta--gtttgtatcaattcaaca-gctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
|||||    |||||  | |    ||  |  |  | | | |||||     | ||     |   |   | |        ||    | |||||||||||||| |||||||||| ||| | ||||| ||||| || ||||| || ||||| || ||||||||||| || |||||||| ||||||||  || | ||||
gtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtgttgtatagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
-gtaagccttttgtataaatgtt-cttagtttgtatcaattcaaca-gctgaaaaataaatcagtgaaaactagtatggctt---------cttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
 || |  |  |  | |  || || | ||   |  | ||    | || | |      | |  | ||  |   |  ||     |          || | ||||||||| ||||| |||| || ||||| || || ||||| ||||| || ||||| |||||||||||||| || ||||| |||||||||||  |  | ||||
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
------------gtaagccttttgtata---aatgttcttagtttgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
                |   |||| |     |||||    ||  ||   ||    |  || ||  |       | |   |   ||   || | |  | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | ||||
acttactccacctctgggactttgaacgtccaatgtggagagcctgg--cagccgaggaggtgggaggctttcctgctcat-ttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G370521_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gtaagccttttgtataa----------atgttcttagtttgt-atcaattcaacagctgaaaaataaatcagtgaaaactagta-tggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
                                                                                                   ||   ||  ||||  |          || |   ||||||||  ||||| | | |  |||   |||  |   ||   | |  |  || | |  | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | ||||
gtacgtactggtctaattaaaggtgcatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatatgtagtttgttgtcaatcccata-ttgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G417650_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gtaagccttttgtataa----------atgttcttagtttgt-atcaattcaacagctgaaaaataaatcagtgaaaactagta-tggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
                                                                                                   ||   ||  ||||  |          || |   ||||||||  ||||| | | |  |||   |||  |   ||   | |  |  || | |  | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || |||||||| ||||||||  || | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagcattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcccata-ttgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G482077_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gtaagccttttgtataa----------atgttcttagtttgt-atcaattcaacagctgaaaaataaatcagtgaaaact-agtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
                                                                                                   ||   ||  ||||  |          || |   ||||||||  ||||| | | |  |||   |||  |   ||   | | | | || | |  | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || |||||||| |||||||   |  | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatctgtagtttgttgtcaatcccata-ttgatgcatactttcctgctcatttattctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGATCTGAGAACAA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
gtaagccttttgtataaatgttcttagtt-tgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
|| ||   |||   |||  ||   |  |  | |  | ||   | |  | |    ||  | | | |    |  | || | | |    ||||||||| ||||| |||| ||  | || ||||| ||||| |||||||||||||| |||||||||||||| || |||||||| ||||||||  |  | ||||
gttagtgattttcttaacggtcactgatgatatgcctatgacataa-taagttgtagcttactcattgatt-tgtgtcctgtatattagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA

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

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
gtaagccttttgtataaatgttcttagtttgtatcaat--tcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
          | |  ||     |  |||||   | | |   ||  | | | | | || || |   |    |  | || |||  || |  ||| ||||| ||| | || ||||| |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| ||||||||||| || ||||| |
---------gtatgcaagcacaca-agtttactttagtaaccactaccggcacagtatat-accaactttttttttgactttctgca--gGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA

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

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 3
gtaagccttttgtataaatgttcttagtttgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
||| ||       | || | | |||   | |||   | |  || |    |  ||| | ||        |  | || |||  || |  ||| ||||| ||| | || ||||| |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| ||||||||||| || | ||| |
gtatgcaagc-acacaagtttactt---tagtaatcact--accggcacagtatataccaacttctttttttttgactttctgca--gGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCACACTA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 14
gtaagccttttgtataaatgttcttagtttgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
           ||||  | |     || ||  || | |  ||   |||       | |       ||||    | |  | |  |  |||| ||||| ||| | || ||||| |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| |||||||||||  | ||||| |
-----------gtatgcaagcagacaggttacattagt--aaacactgttggtacagtgtacaccaactgtctttgactttc-tgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 2
gtaagccttttgtataaatgttcttagtttgtatcaat--tcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
          | |  ||     |  |||||   | | |   ||  | | | | | || ||          |  | || |||  || |  ||| ||||| ||| | || ||||| |||||||| ||||||||||| || ||||  |||||||| |||||||| ||||| ||||||||||| || ||||| |
---------gtatgcaagcacaca-agtttactttagtaaccactaccggcacagtatataccaacttctttttttgactttctgga--gGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCACAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G438355_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------gtaagccttttgtataa--atgttcttagtttgt-atcaattcaacagctgaaaaataaatcagtgaaaactagt-atggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
                                                 |    ||     |  |  || ||  ||||||||  ||||||| | |  |||   |||  |   ||   | |  | ||| | |  | | ||||||||| ||||| |||| |||  ||| || ||| | || ||||| |||||||| |||||||||||||| |  |||||||| ||||||||  |  | | ||
gtaagttatagtagtgttgtgattcatgtacattttctacttatttcaattgtactaggacaccaccatatttgtagtttgttgtcaattccata-ttgatgcatactttcttgctcatttatcatgccctagtttttagGTTGATGGCATGCTGGGAAGGCAGGAGAACCCTAGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTCTATGGTGAACTGGGATGGTCTCAGAAGAA

upper sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 23
gtaagccttttgtataaatgttcttagtttgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
|| |||  ||  ||||| | || || |||| |||    |     |||          |   |  |  ||    | | ||  | | ||||||||||||||| ||||| ||||||| ||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| || ||||||||||| |||||||
gtgagc--ttcatataactcttttt-gtttatata---ttgtttgcttcctctctgcttgctatattct----ttgtttggtct-tagGTTGATAGCATGCTGGGCCGGAGGGAGAATCCAGGGGAACATGAGGCCATGCGTAAGATGAAAAACGAATTTATGGTCAACTGGGATGGCTTGCGCACAA

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|15338257|gb|BI498913.1|BI498913
EST:     TTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA                         GTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
genomic: TTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAAgtaagccttt ... tcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
EST: gi|151404219|gb|EV274029.1|EV274029
EST:     ATTTGTTGACGAA                         GTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
genomic: ATTTGTTGACGAAgtaagccttt ... tcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
EST: gi|27427279|gb|CA938799.1|CA938799
EST:     TTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA                         GTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
genomic: TTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAAgtaagccttt ... tcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
EST: gi|192318122|gb|FK010946.1|FK010946
EST:     TTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA                         GTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG
genomic: TTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAAgtaagccttt ... tcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA
                                           cttcttgt  CT-rich tract
             tgaaaaataaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccttttgtataaatgttcttagtttgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA

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