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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaccgtttataatacctgtcctgttattaattagagcattgatgtggatctttctttgcatgtttaaatcataagataatcatccttaatgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC

Basic information

species Glycine max
transcript GLYMA12G09250.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------------------tcaccgtttataata-cctgtcctgttattaattagagcattgatgtggatctttctttg-catgtttaaatcat-aagataatca--tccttaatgtaa-gttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC
                                                                                     |  |  | || |  | | ||     ||||   ||       |        |   | ||||  |||| | |   || |||  | | |  ||||||| | |  ||||||||| |||||||||||||||||||||||||| || || || ||||| || ||||| |||||||| |||||||| |||||||| |||||| | |||   | 
gtatcctttcatttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgttagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGGTTGTTTTGGCTGGAGAACTTTTGAGGGAGGCTGAAAAGTTAGTTAACAT

upper sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g48290.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------------tcaccgtttataatacctgtcctgttattaattagagcattgatgtggatctttctttgca-tgtttaaatcataagataatcatccttaatgtaag--ttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC
                                                                                        ||||    |  | |    | ||| ||| || | ||  ||| |  |  |||||  | ||   |||| | || |   |  ||||||||||  |  | |||||| |||||||| |||||||| ||||| || ||||||||||| || |||||||| ||||||||||| ||||| ||||| || |||||| ||||    | 
gtatcctttaatttgacccttttttattgctacaccggttaggtaatatcactgttttaaatctctgtttcatatgtatgaagtgttttttacttcatatttttgataatttattggatc-ttcttgttggccaatctttataatgcaaaaataaaaaaaagttattccttaatgtgggcctcagACATCTCAAAAGTGCAAGATGACGAAGTAGGTGATGGAACTACTTCTGTTGTTGTTTTGGCTGGTGAGCTTTTGAGGGAAGCTGAAAAGTTGGTAAATAT

upper sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 3
--tcaccgtttataatacctgtcctgttattaattagagcattgatgtggatctttctttgcatgtttaaatcataagataatcatccttaatgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC
    ||    |||  | | |||    | |||        | |   |    || ||  ||| |   |  ||   | | |  | |  |||||||||    |||||||| |||||||||||||||||||||||||| ||||| || || || ||||||||  | ||||| |||||||| | |||||| || ||| |  ||   | 
ttaaacttcatattctgcttgtgacctcatttggcccctcttctgtacaaatattattttcctaatgaaag--aaaggccattactccttaatgatcattagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGATGGGACAACTTCTGTTGTTGTTCTAGCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACAT

upper sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 5
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 12
tcaccgtttataatacctgtcctgttattaattagagcattgatgtggatctttctttgcatgtttaaatcataagataatca-tccttaatgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC-----------------------------
                                                                 | ||  | | |  | |   |||||||||   | ||||||| |||||||||||||||||||||||||| ||||| || || || ||||||||  | ||||| |||||||| | |||||| || ||| |  ||   |                              
-------------------------------------------------------------ctaatgaaagaaaggccagttgctccttaatggttgctagacatctcaaaagttcaagatgatgaagttggtgatgggacaacttctgttgttgttctagCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG

upper sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 4
tcaccgtttataata--cctgtcctgttattaattagagcattgatgtggatctttctttgcatg---tttaaatcataagataat-catccttaatgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC
     || | ||||   ||||     || |    |  ||  || |  |   | |||  ||   ||   |||   ||| |      |  |||     |||   | |||||| || ||||||||||||||||| ||||| |||||||||||||| |||||||| ||||| || || ||| | ||||| ||||||||||| || ||  |
-----gtatgtaatttccctgcgacattctggcatgaagttttcacattcgttttttcttagttgggttttctctcacagttcgttgtatctggtttgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC

upper sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
-tcaccgtttataatacctgtcc---tgttattaattagagcat-tgatgtggatctttctttgcatgtttaaatcataagataatcatccttaatgtaagt--tagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC
 |     | |  |||||    ||   ||  | |  ||| | |   ||||  || |  |        |  ||    |||  |||  |||||||||||  |||    ||| ||||| ||||||||||||||||| ||||| ||||| || || ||||||||||| |||||||| || |||||||| || ||||| ||| ||||      
gtatagatgtgaaatacaaagccatctggaactttttataacccatgattaggcttataaaagttgtagtttg-ccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------

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|7591500|gb|AW707232.1|AW707232
EST:     AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTG                         ACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
genomic: AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTGgtatccttgt ... tgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
EST: gi|207783070|gb|GD751071.1|GD751071
EST:     AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTG                         ACATATCAAAAGTTCAAGAATGATGAAG
genomic: AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTGgtatccttgt ... tgtaagttagACATATCAAAAGTTCAAGA-TGATGAAG
EST: gi|7587973|gb|AW703779.1|AW703779
EST:     AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTG                         ACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
genomic: AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTGgtatccttgt ... tgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
EST: gi|15200734|gb|BI424502.1|BI424502
EST:     AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTG                         ACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
genomic: AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTGgtatccttgt ... tgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
EST: gi|213601247|gb|DB956527.1|DB956527
EST:     AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTG                         ACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
genomic: AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTGgtatccttgt ... tgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
EST: gi|261497099|gb|GT185167.1|GT185167
EST:     AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTG                         ACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
genomic: AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTGgtatccttgt ... tgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTG
EST: gi|208198857|gb|GD998538.1|GD998538
EST:     AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTG                         ACATATCAAAAGTTCAAGATGATGAAG
genomic: AATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTGgtatccttgt ... tgtaagttagACATATCAAAAGTTCAAGATGATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatctttctttgcatgtttaaatcataagataatcatccttaatgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC
                                     atccttaat  putative branch site 
               atgtttaaatcataag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaccgtttataatacctgtcctgttattaattagagcattgatgtggatctttctttgcatgtttaaatcataagataatcatccttaatgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - -tgtcctg
- - - - - - - - - - - - - - - - - - - - -gatgtgg