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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatggtaactcaatggaactctgatttacccttattgaatataacttttcatgttagtttgcatgttgtatctgattgatttctcttcatatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGGACAGGCACTTATAGCATGGTTCTCTCAAAGGCTGCATTCTTTCACAGGA

Basic information

species Glycine max
transcript GLYMA16G32650.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32650.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g49150.1 (Oryza sativa), 3'ss of exon 2
-tgatggtaactcaatggaactctgatttacccttattgaatataacttttca-tgttagtttgcatgttg--tat-ctgattgatttctcttcatatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGGACAGGCACTTATAGCATGGTTCTCTCAAAGGCTGCATTCTTTCACAGGA
 | || |    | | |  |    ||  |  |   |  |   | ||| |  | | | ||| |  | | |||   ||| |  ||||   | ||| | |   || |||  ||  |||||     | ||||| |||||| | |||||||| |||||||||||||| |||||||||||||||||||| || ||    || || |||||| 
ctaattgaggatgactaca--catgggtggctacttcttggtgtaattgctgaattttattgaggaagttagttatgccaattggagtgtctgctt---ctgcagGGAAGTAATGCAAAGGAATACAGATATGGAAGCTGGTGGTCAGTTTGGTGGACAGGGACTTATAGCATGGTTCTCTCCAAAGCAAGTTTTTTCCACAGGC

upper sequence: GLYMA16G32650.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G347766_T01 (Zea mays), 3'ss of exon 2
-------tgatggtaactcaatggaactctgatttacccttattgaatataacttttcatgttagtttgcatgttgtatctgattgatttctcttcatatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGGACAGGCACTTATAGCATGGTTCTCTCAAAGGCTGCATTCTTTCACAGGA
       ||     || | ||   |       |||   | | |||||    |  | | |    |      || ||        ||| | | |||||      | |||  || || ||  |     ||| | || ||| | |||||||| |||||||||||||| || || ||||||||||| || || || |  ||||| |||| ||
gttggtttggcacaaattaaacaaagaataagtttgaacatgttgaaggatatatgtaaaaaaaaacaa-atcttaaccggagttgttgtttcttc------tgcagAGAAGCACTGAAGATGCATACCGATACGGAAGCTGGTGGTCAGTTTGGTGGACAGGGACATACAGCATGGTTCTTTCCAAAGCGGGGTTCTTCCACAAGA

upper sequence: GLYMA16G32650.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S87_187V6.1 (Physcomitrella patens), 3'ss of exon 2
-tgatggtaactcaatggaactctgatttacccttattgaatataacttttcatgttagtttgcatgttgtatctgattgatttctcttcatatactaca-gCAAAACAATGCT-----GCAT----ATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGGACAGGCACTTATAGCATGGTTCTCTCAAAGGCTGCATTCTTTCACAGGA
 |  |       |||||  |   |   | ||  |   | |||  ||| |||||||   ||| |    || |  || ||| | || |||   ||    |    || ||   | |      | ||    | ||||| ||||||||||||||||| || |||||||  || ||||||||||||||  | ||||| ||||| ||  |||      
tttctttctttgcaatgttatctttgctaacagtctattaatg-aacctttcatg--ggttcg-ggattatg-cttattcacttttctgtgtaattgatgcacagAATCTTCCCCTTGGGAATTATGAATACAGTTATGGAGGATGGTGGTCAGTGTGGTGGATGGGTACTTATAGCATGGTGTTATCAAAAGCTGCTTTTATTC------

upper sequence: GLYMA16G32650.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ36641 (Selaginella moellendorffii), 3'ss of exon 2
tgatggtaactcaatggaactctgatttacccttattgaata-taacttttcatgttagtttgcatgttgtatctgattgatttctcttcatatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGGACAGGCACTTATAGCATGGTTCTCTCAAAGGCTGCATTCTTTCACAGGA
                           |||    |  ||| |  ||  | ||     ||||| | |    | ||   ||| ||| |||  | |  | |   | |    |  || |   ||||| ||||||||| |||||| ||||||||||||| ||  | || ||||||||||| || ||||  || |||||||      
--------------------------gtactgggaaggaaaaacaaaatctctcaacagttt-cttacactttcc--ttggtttttctctagAGCCAAATTCCAGCGCAAACTAC---TTACAAGTATGGAGGGTGGTGGACTGTTTGGTGGACTGGATCATACAGCATGGTTCTTTCCAAGGTCGCGTTCTTTC------

upper sequence: GLYMA16G32650.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ18074 (Selaginella moellendorffii), 3'ss of exon 2
tgatggtaactcaatggaactctgatttacccttattgaatataacttttcatgttagtttgcatgttgtatctgattgatttctcttcatatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGGACAGGCACTTATAGCATGGTTCTCTCAAAGGCTGCATTCTTTCACAGGA
                       |   |          || | ||  |||||      ||  ||  ||     |  ||| ||| |||  | |  | | | | |    |  || |   ||||| ||||||||| |||||| ||||||||||||| ||  | || ||||||||||| || ||||  || |||||||||    
-----------------------gtactgggaaggaaaaacaaaatctttca-acagtttctcacatt----ttccttggtttttctctagagCCAAAATCCAGCGCAAACTAC---TTACAAGTATGGAGGGTGGTGGACTGTTTGGTGGACTGGATCATACAGCATGGTTCTTTCCAAGGTCGCGTTCTTTCAC----

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|193628488|gb|FK575828.1|FK575828
EST:     CATTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAG                         CAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGG
genomic: CATTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAGgttagttatt ... tatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGG
EST: gi|208269223|gb|GE070246.1|GE070246
EST:     CATTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAG                         CAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGG
genomic: CATTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAGgttagttatt ... tatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGG
EST: gi|208265149|gb|GE061753.1|GE061753
EST:     CATTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAG                         CAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGG
genomic: CATTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAGgttagttatt ... tatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGG
EST: gi|208223351|gb|GE024848.1|GE024848
EST:     CATTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAG                         CAAAATAATGCTGCATATTACAGG
genomic: CATTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAGgttagttatt ... tatactacagCAAAACAATGCTGCATATTACAGG
EST: gi|15286710|gb|BI470601.1|BI470601
EST:     CTCGAATTCACTGGCTGGATAAGGAG                         CAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGG
genomic: CTCGAATTCACTGGCTGGATAAGGAGgttagttatt ... tatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGG
EST: gi|207760183|gb|GD731896.1|GD731896
EST:     CGTTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAG                         CAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTGTGGTGG
genomic: CATTTACGATGGTGGGATTTGTTCCTCGAATTCACTGGCTGGATAAGGAGgttagttatt ... tatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcatgttagtttgcatgttgtatctgattgatttctcttcatatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGGACAGGCACTTATAGCATGGTTCTCTCAAAGGCTGCATTCTTTCACAGGA
                             gattgat  putative branch site (score: 4)
                                   tttctcttcat  CT-rich tract
                              attgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatggtaactcaatggaactctgatttacccttattgaatataacttttcatgttagtttgcatgttgtatctgattgatttctcttcatatactacagCAAAACAATGCTGCATATTACAGGTATGGAGGATGGTGGTCTGTTTGGTGGACAGGCACTTATAGCATGGTTCTCTCAAAGGCTGCATTCTTTCACAGGA

-gatggta
- - - - -ctcaatg
- - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg