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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacttctaggaattctatgtggaggcattttctgatgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG

Basic information

species Glycine max
transcript GLYMA12G32850.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g01060.1 (Oryza sativa), 3'ss of exon 3
gtatacttctaggaattctatgtggaggcattttctgatgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG------
                                                 |   || |   | ||||||  |   ||  |  |   |     |  |      |||  |  |   || ||||||||| |||||||| |||||||| |||||| | ||||||||||| ||||||||||     ||  ||| | || |  | | |  |  || | |||  |||      
------------------------------------------------gtaaatcttgcttctcatttgatgaaatgaggctactgacacatccatgctctaattctgatatgttacagCTATGCCATCAAGAAGAAGGATGAGATTGAGCGTGTTGCCAAGGCGAACCGTTGAG-----TGCTGAACCCATCTCAGTG-TGCTCGAGCTATTGCCTTGCACTGT

upper sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g29190.5 (Oryza sativa), 3'ss of exon 2
gtatacttctaggaattctatgtggaggcattttctgatgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttac-cgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGC------------TTGTG--GAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG-----------------------------
                                                               | |||| ||    || |    || | ||   ||       ||   | |   |||||||||||| |||||||| |||||||| || ||| | ||||||||||| ||||||||||  |             |||||   ||||  |      | |||  | || | |  |||                              
---------------------------------------------------------------ctttttgttcggatgataccaggttattgacacatctgtgatctaattgtgtttcagctatgccatcaagaagaaggatgagatcgagcgtgttgccaagGCCAACCGTTGAGTGGTGATCCCATGTCATTGTGCTAAAGCTCTTGCGCTGTTTGGCAGGACTATACTTTTTGCTAGTAATTTAAGCCTTTTCAGACCTA

upper sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g29190.4 (Oryza sativa), 3'ss of exon 3
gtatacttctaggaattctatgtggaggcattttctgatgtattttattttctt--catctctttcatttttttttattggtgtttgggtttttttac-cgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG-
                                      |  |    ||| || |   |  |||| | |||| ||    || |    || | ||   ||       ||   | |   |||||||||||| |||||||| |||||||| || ||| | ||||||||||| ||||||||||  |       | |  || | ||| |  |         ||||| | 
-------------------------------------gtacaacacattgtcatggtacatcttgctttttgttcggatgataccaggttattgacacatctgtgatctaattgtgtttcagCTATGCCATCAAGAAGAAGGATGAGATCGAGCGTGTTGCCAAGGCCAACCGTTGAGTGGTGATCCCATGTCAT-TGTGCTAAAGCTCTTGCGCTGTTTGGC

upper sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G078985_T01 (Zea mays), 3'ss of exon 3
gtatacttctaggaattctatgtggaggcattttctgatgtattttatttt-cttcatctctttcatttttttttattggtgtt-tgggtttttttaccgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG-
                                     || |||  | | |  ||  || |  ||  ||||||  |||  | | | ||  || |  |     |    ||| ||   |  |||||| || |||||||| ||||| || |||||| | ||||||||||| ||||||||||  |    || |  |    |   |       |  | |  ||||   
---------------------------------gtatatatatcctgtctggctatatttggttgtttttttcctatctgcgatgtgaattgtgctcattcatggcaattctt-gtcacagCTACGCCATCAAGAAGAAGGACGAGATTGAGCGTGTTGCCAAGGCCAACCGTTGAGTGGAGCTTGTATCCTG-GTGCACTTGCACTAGAACTACGTTTCTG

upper sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G37270.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatacttctaggaattctatgtggaggcattttctg-atgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATA--TTTGCG--ATTGTGAAGATTTTGTTTTG
                     ||     || | | |  |  || | | | | ||| ||  |||   ||| || ||| |  |  ||  | |    ||     |  |  |  |   || ||||||||| |||||||| || ||||| |||||||||||||| ||||| || |||| ||     |       |  ||  |||||   ||    |||| ||| |    
---------------------gtaagaacactctatctacatagtctgtct-cttgatggcttcactttattgttagt--tagttaagctaa--taatagcatcttctcttgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTT----

upper sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatacttctaggaattctatgtggaggcattttctgatgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaa-aaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG-
                                       |||  |    |||   ||  ||| || | || || ||     ||   ||     ||  ||   ||   |  |   || ||||||||| |||||||| |||||||| ||||| |||||||||||||| || |||| || |  ||      ||  | |  |  |   |   | | |   |  | 
---------------------------------------gtaaatacacttccaaatgactt-cactattgttcatataacttaaagtgaagctaatgattgaactgttatgtcttgcagCTATGCCATCAAGAAGAAGGATGAGATTGAAAGAGTTGCCAAGGCTAATCGTTAAGGATTTTCCCTTTGCCCTGTGCGTTACAATCTCG-TATCAATGAGT

upper sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16239 (Selaginella moellendorffii), 3'ss of exon 4
gtatacttctaggaattctatgtggaggcattttctgatgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG-
                                       |||  ||     |   |  ||||||  |    |  |  | | |   | |  || |         | ||      |||||||||||| |||||||||||||| || |||||| | ||||| ||||| || ||||||| | |   |   |    ||||     || |   |  | | ||||| 
---------------------------------------gtaccttgcggccagaaattctttctctcgcctcaa--gctctaaagttccttgtttttgtttttgatg-----tttcagCTATGCGATCAAGAAAAAGGACGAGATTGAGCGTGTTGCGAAGGCGAATCGTTGAGAAACACATTCTAATG-TATTGAGCCTTTTTTGGCATATCTTTTGA

upper sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ17708 (Selaginella moellendorffii), 3'ss of exon 4
gtatacttctaggaattctatgtggaggcattttctgatgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG-
                                       |||  |      |   |  |||| |  |    |  |      | |    ||  ||            |      |||||||||||| ||||||||||||||||| |||||| | ||||| ||||| || ||||||| | |   |   |     ||   |  || ||   || |  ||    
---------------------------------------gtacctcgcggccagaaattcttcctctcgcctcaagc----tctaaagttccttgtt---------tttgatgtttcagCTATGCGATCAAGAAAAAGGATGAGATTGAGCGTGTTGCGAAGGCGAATCGTTGAGAAACACATTCTAATGTAATGAACCTTTTTGGC-ATATCATTCGAA

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|6095006|gb|AW119673.1|AW119673
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTTTTGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACC
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTAT-GCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACC
EST: gi|254347062|gb|GR856732.1|GR856732
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|57574861|gb|CX547836.1|CX547836
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|151400398|gb|EV270212.1|EV270212
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|151394461|gb|EV264332.1|EV264332
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|254347061|gb|GR856731.1|GR856731
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|31468288|gb|CD410316.1|CD410316
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|298166882|gb|HO010321.1|HO010321
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCATCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|6718846|gb|AW306493.1|AW306493
EST:     AATGCTNGGCTGATGAAACT-ATTAATGCA-CANAAGG-TCGTCCA-CAG                         CTATGCTATCAAG
genomic: AATGCTTGGCTGATGAA-CTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAG
EST: gi|193420352|gb|FK388290.1|FK388290
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|208240513|gb|GE035983.1|GE035983
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|192294201|gb|FG986290.1|FG986290
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAG-ATGAAATTGAGAGAGTTGCCAAAGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|58015968|gb|CX702710.1|CX702710
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|33388884|gb|CA852091.1|CA852091
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAG
EST: gi|13482102|gb|BG511445.1|BG511445
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTNTCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|42722858|gb|CK768757.1|CK768757
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|18730141|gb|BM525707.1|BM525707
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAA
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAA
EST: gi|5819946|gb|AI988083.1|AI988083
EST:     AATGCTTCGCTGATGAACTTATTTATGCAGCANAAAAG-TCGTCCAACAG                         CTATGCTATCAAGAGAAAG
genomic: AATGCTTGGCTGATGAACTTATTAATGCAGCA-AAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAG
EST: gi|192324473|gb|FK016424.1|FK016424
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
EST: gi|209696973|gb|BW660538.1|BW660538
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAG
EST: gi|13787819|gb|BG650411.1|BG650411
EST:     GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAG                         CTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG
genomic: GAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttct ... tccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttttttattggtgtttgggtttttttaccgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG
                                            ctccatttc  CT-rich tract
                       tttttttaccgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacttctaggaattctatgtggaggcattttctgatgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaaaaataatactccatttcagCTATGCTATCAAGAAAAAGGATGAAATTGAGAGAGTTGCCAAGGCAAACCGTTGAGCAGCTTGTGGAAGCAATATTTGCGATTGTGAAGATTTTGTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA