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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtgagttatgcatctctatattattacatatgcctgtattgtccattatttagcattgggttgttaattgtatatattaaattcctttttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAAACAGGATTTCTGGGTAGTAGGATAAAGTGGAATTTCACTAAGT

Basic information

species Glycine max
transcript GLYMA19G33650.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G33650.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 4
aagtgagtt-atgcatctctatattattacatat-gcctgtattgtccattatttagcattgggttgttaattgtatatattaaattcctttttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAAACAGGATTTCTGGGTAGTAGGATAAAGTGGAATTTCACTAAGT
| |||  || ||        | |||  ||||| | ||    ||  |    | |  |   ||   |   ||||  || || || |||||  |||| | || |||| ||||| ||||| |||||| | ||||| |||||||||||||| |||||| | ||||  |||||||| ||   |||||| || ||||||||||| ||||
atgtgtctttattgggtctcaaatttctacattttgctccgatcataggatttacatagttaaat--ataatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT
















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|298171406|gb|HO016438.1|HO016438
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|9819421|gb|BE554934.1|BE554934
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|10709776|gb|BF009500.1|BF009500
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|13477752|gb|BG507504.1|BG507504
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298166996|gb|HO010435.1|HO010435
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|15663056|gb|BI700427.1|BI700427
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|208048673|gb|GD846232.1|GD846232
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|9820763|gb|BE556273.1|BE556273
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|19453002|gb|BM954412.1|BM954412
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|208115002|gb|GD910359.1|GD910359
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298187303|gb|HO034452.1|HO034452
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298197094|gb|HO041837.1|HO041837
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298173934|gb|HO017270.1|HO017270
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298168059|gb|HO013322.1|HO013322
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298194861|gb|HO043333.1|HO043333
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298192806|gb|HO033240.1|HO033240
EST:     AGGAATTTGCCTATACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298184031|gb|HO029244.1|HO029244
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|151397536|gb|EV267409.1|EV267409
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|192319134|gb|FK009102.1|FK009102
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298166854|gb|HO010293.1|HO010293
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|193433477|gb|FK403997.1|FK403997
EST:     GGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: GGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCA-TTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298166545|gb|HO009984.1|HO009984
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|207711242|gb|GD693019.1|GD693019
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAA
EST: gi|298195273|gb|HO043801.1|HO043801
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|207802831|gb|GD776144.1|GD776144
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298183535|gb|HO028748.1|HO028748
EST:     AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCCGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGTACAAGGTACAAGGCTGAGTATCCCATTTTTGGAAAGgtaaggtatt ... ttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatttagcattgggttgttaattgtatatattaaattcctttttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAAACAGGATTTCTGGGTAGTAGGATAAAGTGGAATTTCACTAAGT
                  tgttaat  putative branch site (score: 3)
                                      ttcctttttatttac  putative PPT
                 ttgttaattgtatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtgagttatgcatctctatattattacatatgcctgtattgtccattatttagcattgggttgttaattgtatatattaaattcctttttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAAACAGGATTTCTGGGTAGTAGGATAAAGTGGAATTTCACTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - tatgcat
- - - - - - - - - - - - - - - tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggttg