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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaataattgaaaaagtagcttctgtaatctgcttcttagtcactgcttgcatgccactcaatggactggaaccatattatgctgctgtaagggacagtggaaccatattattcttttttgaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT

Basic information

species Glycine max
transcript GLYMA13G39210.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g33080.1 (Oryza sativa), 3'ss of exon 3
gtaaaataattgaaaaagtagcttctgtaatctgcttcttagtcactgcttgcatgccactcaatggactggaaccatattatgctgctgtaagggacagtggaaccatattattcttttttgaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT
                              |  ||||     ||| | |||| || |   |||   | |   || ||   |||  || | ||           | || |||  ||| || ||   |||||       ||  | || ||||||||||| ||| | |  || || ||||| || ||||| || |||||||| |||||||||||||| ||||||  |||||| |||||||||
-----------------------------gtaggcttgcc--tcattacttg-attcttgtcaggagtccacaagcaatgtata-tgttctatttctgtagttatccctatgcttcattctttcttgttcg----atagGTTTCAAAAACTTGCAAAGGAGCTGGAAGTTGTAATACCTGTCAGCTTTTTTGAGGAGGCGAACAATGCACATTACAATTCAGTAGCCATTATTGATGCT

upper sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaaaataattgaaaaagtagcttctgtaatctgcttcttagtcactgcttgcatgccactcaatggactggaaccatattatgctgctgtaagggacagtggaaccatattattcttttttgaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT
                                      |  | || |||||    |      || | | |  |     ||   | ||     | | ||  |  |    | | ||  ||   ||  |     | |  ||| |||||||| || ||||| || || |||||||| ||||| ||||| ||||| ||||||||||| | ||||||||| ||||| |  || ||||||||||||
-------------------------------------gtgtgacattgcttatccgatttctaacgcagtaaagtggaatctcgatgtatctatgtactatctagtgttttaatggttggatggtttaatttaacacagGATGCAGAAGCTGGCAAAGGAATTGGGTGTAGTGATACCTGTTAGTTTCTTTGAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCT

upper sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------gtaaaataattgaaaaagtagcttc-tgtaatctgcttcttagtcactgcttgcatgccactcaatggactgga-accatattatgctgctgtaagggacagtggaaccatattattctt---ttttgaatgttcatg--atgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT
                                     | |  || ||| ||    | | || |||| |     |||| ||      ||  ||  |||   |   |  ||| | | |    | || ||  |    ||| |  || ||  ||   |||   || |  || | ||||  |||||| ||||| ||||||||||||||||| || ||||| ||||||||||||||||| || |||||||||||||| ||||| |||||||  |||||| ||||||||
gtaaatgtttcaacccaaacctggcttctagatttgctcagctagttggaatgtcatcctcctgtactaattatcttcgt----atttttatagcacaggaacaaaaggacatcttgaattcctactacattt-acaatttaatcaagttgaacttatgttgtacatctgcatgctatgcagGATGCAAAAACTTGCAAAAGAGTTGGGAGTAGTGATACCAGTTAGCTTCTTTGAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCT

upper sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ07601 (Selaginella moellendorffii), 3'ss of exon 3
gtaaaataattgaaaaagtagcttctgtaatctgcttcttagtcactgcttgcatgccactcaatggactggaaccatattatgctgctgtaagggacagtggaaccatattattcttttttgaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT
                                                                             | || | ||  ||  |||     ||||     |   |||  |||             | ||| ||| || | || || |||||  | || || || || || |||||||||||||||||||||||||||||||| ||||| || |  |  || || ||||| 
--------------------------------------------------------------------------gttttttttccttgtgctaggatttttggagaaggaagtttcggttt-------------tccagGATGAAGGAGCTGGCGAAAGAACTCGGAGTTGTGATTCCTGTTAGCTTCTTCGAGGAGGCAAACAATGCACACTATAACTCTATTGTTATCATAGATGCC

upper sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ10979 (Selaginella moellendorffii), 3'ss of exon 3
gtaaaataattgaaaaagtagcttctgtaatctgcttcttagtcactgcttgcatgccactcaatggactggaaccatattatgctgctgtaagggacagtggaaccatattattcttttttgaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT
                                                                             | ||   ||  ||  |||     ||||     |   |||  |||             | ||| ||| || | || || |||||  | || || || || || |||||||||||||||||||||||||||||||| ||||| || |  |  || || ||||| 
---------------------------------------------------------------------------gttttttcccttgtgctaggatttttggagaagaaagtttcggttt-------------tccagGATGAAGGAGCTGGCGAAAGAACTCGGAGTCGTGATTCCTGTTAGCTTCTTCGAGGAGGCAAACAATGCACACTATAACTCTATTGTTATCATAGATGCC

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|14125523|gb|BG789961.1|BG789961
EST:     GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         AATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
genomic: GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... catgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
EST: gi|15199519|gb|BI423872.1|BI423872
EST:     GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         AATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
genomic: GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... catgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
EST: gi|15813986|gb|BI786261.1|BI786261
EST:     CAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         AATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
genomic: CAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... catgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
EST: gi|209726298|gb|BW659611.1|BW659611
EST:     GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         AATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
genomic: GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... catgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
EST: gi|7924791|gb|AW830817.1|AW830817
EST:     GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         AATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
genomic: GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... catgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
EST: gi|298172516|gb|HO019556.1|HO019556
EST:     GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         AATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
genomic: GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... catgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
EST: gi|298165233|gb|HO011282.1|HO011282
EST:     GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         AATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
genomic: GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... catgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
EST: gi|19935096|gb|BQ080126.1|BQ080126
EST:     GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         AATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
genomic: GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... catgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
EST: gi|209726043|gb|BW672766.1|BW672766
EST:     GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         AATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT
genomic: GAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... catgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctgtaagggacagtggaaccatattattcttttttgaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT
                       atattattcttttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaataattgaaaaagtagcttctgtaatctgcttcttagtcactgcttgcatgccactcaatggactggaaccatattatgctgctgtaagggacagtggaaccatattattcttttttgaatgttcatgatgcagAATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTTATACCAGTTAGCTTCTTCGAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG